From christoph.gille at charite.de Mon Sep 5 04:50:26 2005 From: christoph.gille at charite.de (Dr. Christoph Gille) Date: Mon, 5 Sep 2005 10:50:26 +0200 (CEST) Subject: [BiO BB] need software testing MacOSX and MS-WindowsME Message-ID: <51320.192.168.220.203.1125910226.squirrel@webmail.charite.de> Dear All, If you are interested in protein sequences and structures and have some spare minutes I would appreciate if you could test some system dependent features of my software. It will not take long. Thanks Christoph From pagarwal at linus.ornl.gov Wed Sep 7 20:34:34 2005 From: pagarwal at linus.ornl.gov (Pratul K. Agarwal) Date: Wed, 7 Sep 2005 20:34:34 -0400 (EDT) Subject: [BiO BB] Announcing the release of VigyaanCD v1.0 Message-ID: Vigyaan (http://www.vigyaancd.org/) is an electronic workbench for bioinformatics, computational biology and computational chemistry. New in version 1.0: Based on KNOPPIX v3.7, most software packages updated, new applications added. At present the following ready to use software comes on VigyaanCD: Arka/GP, Artemis, Bioperl, BLAST (NCBI-tools), ClustalW/ClustalX, Cn3D, EMBOSS tools, Garlic, Glimmer, GROMACS, Ghemical, GNU R, Gnuplot, GIMP, ImageMagick, Jmol, MPQC, MUMer, NJPlot, Open Babel, Octave, PSI3, PyMOL, Ramachandran plot viewer, Rasmol, Raster3D, Seaview, TINKER, XDrawChem, Xmgr and Xfig. GNU C/C++/Fortran compilers and additional Linux tools (such as ps2pdf) are also available. VigyaanCD also provides tools required to compile and install other applications (from source). Therefore, making testing of 'Linux' applications possible on computers with other OS. From christoph.gille at charite.de Thu Sep 8 05:48:01 2005 From: christoph.gille at charite.de (Dr. Christoph Gille) Date: Thu, 8 Sep 2005 11:48:01 +0200 (CEST) Subject: [BiO BB] Announcing the release of VigyaanCD v1.0 In-Reply-To: References: Message-ID: <61274.84.190.20.184.1126172881.squirrel@webmail.charite.de> great, has it a similar scope as bioknoppix ? What I do not like in Bioknoppix is that it is KDE based. This means that it runs only on the edge of newest hardware technologies. Is LaTeX included ? Cheers Christoph Am Do, 8.09.2005, 02:34, schrieb Pratul K. Agarwal: > Vigyaan (http://www.vigyaancd.org/) is an electronic > workbench for bioinformatics, computational biology and computational > chemistry. New in version 1.0: Based on KNOPPIX v3.7, most software > packages updated, new applications added. > > At present the following ready to use software comes on > VigyaanCD: Arka/GP, Artemis, Bioperl, BLAST (NCBI-tools), > ClustalW/ClustalX, Cn3D, EMBOSS tools, Garlic, Glimmer, > GROMACS, Ghemical, GNU R, Gnuplot, GIMP, ImageMagick, Jmol, > MPQC, MUMer, NJPlot, Open Babel, Octave, PSI3, PyMOL, > Ramachandran plot viewer, Rasmol, Raster3D, Seaview, TINKER, > XDrawChem, Xmgr and Xfig. GNU C/C++/Fortran compilers and > additional Linux tools (such as ps2pdf) are also available. VigyaanCD also > provides tools required to compile and install other applications (from > source). Therefore, making testing of 'Linux' applications possible on > computers with other OS. _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > From golharam at umdnj.edu Thu Sep 8 12:11:50 2005 From: golharam at umdnj.edu (Ryan Golhar) Date: Thu, 08 Sep 2005 12:11:50 -0400 Subject: [BiO BB] FW: [blast-announce] [BLAST-Announce #51] Automatic BLAST Database Update Script Message-ID: <033f01c5b490$058a57d0$d33d140a@GOLHARMOBILE1> FYI for those of you who haven't seen this... -----Original Message----- From: blast-announce-bounces at ncbi.nlm.nih.gov [mailto:blast-announce-bounces at ncbi.nlm.nih.gov] On Behalf Of Mcginnis, Scott (NIH/NLM/NCBI) Sent: Thursday, September 08, 2005 10:16 AM To: 'blast-announce at ncbi.nlm.nih.gov' Subject: [blast-announce] [BLAST-Announce #51] Automatic BLAST Database Update Script We are pleased to announce the new automatic downloader for BLAST preformatted databases. http://www.ncbi.nlm.nih.gov/blast/docs/update_blastdb.pl Database sets may be retrieved automatically with update_blastdb.pl. Documentation for the update_blastdb.pl script can be obtained by running the script without any arguments (perl is required). The script will download multiple volumes for database if they exist, with having to designate each volume. For example: ./update_blastdb.pl htgs This command will download all the HTGs files htgs.00.tar.gz - htgs.03.tar.gz The script can also compare your local copy of a database and only download files if the date stamp has changed reflecting a newer version of the database. This will allow the script run on a schedule and only download files when needed. If you have any questions please contact blast-help at ncbi.nlm.nih.gov. NAME update_blastdb.pl - Download pre-formatted BLAST databases from NCBI SYNOPSIS update_blastdb.pl [options] blastdb ... OPTIONS --passive Use passive FTP, useful when behind a firewall (default: false). --timeout Timeout on connection to NCBI (default: 120 seconds). --force Force download even if there is a archive already on local directory (default: false). --verbose Increment verbosity level (default: 1). Repeat this option multiple times to increase the verbosity level (maximum 2). --showall Show all available pre-formatted BLAST databases (default: false). The output of this option lists the database names which should be used when requesting updates or downloads using this script. --quiet Produce no output (default: false). Overrides the --ver- bose option. DESCRIPTION This script will download the pre-formatted BLAST databases requested in the command line from the NCBI ftp site. EXIT CODES This script returns 0 on success and a non-zero value on errors. BUGS Please report them to COPYRIGHT See PUBLIC DOMAIN NOTICE included at the top of this script. 2005-08-08 perl v5.6.1 UPDATE_BLASTDB(1) From pavlidis at egeeninc.com Tue Sep 6 02:21:22 2005 From: pavlidis at egeeninc.com (Pavlos Pavlidis) Date: Tue, 06 Sep 2005 09:21:22 +0300 Subject: [BiO BB] a question about footprinter Message-ID: <431D3562.1050703@egeeninc.com> Hi all, I have downloaded footprinter 2.0 for linux, and when I'm trying to install it, I get the following error message. I'm using debian. Thanks Pavlos pavlidis at metsis:~/FootPrinter2.0$ make g++ -O2 -I. -DSHORT_MOTIFS -c merging.cc In file included from /usr/include/c++/3.3/backward/iostream.h:31, from FootPrinter.h:19, from merging.h:15, from merging.cc:15: /usr/include/c++/3.3/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header. Please consider using one of the 32 headers found in section 17.4.1.2 of the C++ standard. Examples include substituting the header for the header for C++ includes, or instead of the deprecated header . To disable this warning use -Wno-deprecated. In file included from stl/iterator.h:36, from stl/algobase.h:33, from stl/deque.h:30, from FootPrinter.h:21, from merging.h:15, from merging.cc:15: stl/stl_iterator.h:249: warning: `iterator_traits::difference_type' is implicitly a typename stl/stl_iterator.h:249: warning: implicit typename is deprecated, please see the documentation for details stl/stl_iterator.h: In function `typename iterator_traits::difference_type __distance(InputIterator, InputIterator, input_iterator_tag)': stl/stl_iterator.h:250: warning: `iterator_traits::difference_type' is implicitly a typename stl/stl_iterator.h:250: warning: implicit typename is deprecated, please see the documentation for details stl/stl_iterator.h: At global scope: stl/stl_iterator.h:260: warning: `iterator_traits::difference_type' is implicitly a typename stl/stl_iterator.h:260: warning: implicit typename is deprecated, please see the documentation for details stl/stl_iterator.h:266: warning: `iterator_traits::difference_type' is implicitly a typename stl/stl_iterator.h:266: warning: implicit typename is deprecated, please see the documentation for details stl/stl_iterator.h:618: warning: `reverse_iterator::difference_type' is implicitly a typename stl/stl_iterator.h:618: warning: implicit typename is deprecated, please see the documentation for details In file included from stl/iterator.h:39, from stl/algobase.h:33, from stl/deque.h:30, from FootPrinter.h:21, from merging.h:15, from merging.cc:15: stl/type_traits.h:54: error: redefinition of `struct __true_type' /usr/include/c++/3.3/bits/type_traits.h:90: error: previous definition of ` struct __true_type' stl/type_traits.h:57: error: redefinition of `struct __false_type' /usr/include/c++/3.3/bits/type_traits.h:91: error: previous definition of ` struct __false_type' stl/type_traits.h:61: error: redefinition of `struct __type_traits<_Tp>' /usr/include/c++/3.3/bits/type_traits.h:94: error: previous definition of ` struct __type_traits<_Tp>' stl/type_traits.h:93: error: redefinition of `struct __type_traits' /usr/include/c++/3.3/bits/type_traits.h:131: error: previous definition of ` struct __type_traits' stl/type_traits.h:101: error: redefinition of `struct __type_traits' /usr/include/c++/3.3/bits/type_traits.h:139: error: previous definition of ` struct __type_traits' stl/type_traits.h:109: error: redefinition of `struct __type_traits' /usr/include/c++/3.3/bits/type_traits.h:147: error: previous definition of ` struct __type_traits' stl/type_traits.h:117: error: redefinition of `struct __type_traits' /usr/include/c++/3.3/bits/type_traits.h:163: error: previous definition of ` struct __type_traits' stl/type_traits.h:125: error: redefinition of `struct __type_traits' /usr/include/c++/3.3/bits/type_traits.h:171: error: previous definition of ` struct __type_traits' stl/type_traits.h:133: error: redefinition of `struct __type_traits' /usr/include/c++/3.3/bits/type_traits.h:179: error: previous definition of ` struct __type_traits' stl/type_traits.h:141: error: redefinition of `struct __type_traits' /usr/include/c++/3.3/bits/type_traits.h:187: error: previous definition of ` struct __type_traits' stl/type_traits.h:149: error: redefinition of `struct __type_traits' /usr/include/c++/3.3/bits/type_traits.h:195: error: previous definition of ` struct __type_traits' stl/type_traits.h:157: error: redefinition of `struct __type_traits' /usr/include/c++/3.3/bits/type_traits.h:203: error: previous definition of ` struct __type_traits' stl/type_traits.h:165: error: redefinition of `struct __type_traits' /usr/include/c++/3.3/bits/type_traits.h:227: error: previous definition of ` struct __type_traits' stl/type_traits.h:173: error: redefinition of `struct __type_traits' /usr/include/c++/3.3/bits/type_traits.h:235: error: previous definition of ` struct __type_traits' stl/type_traits.h:181: error: redefinition of `struct __type_traits' /usr/include/c++/3.3/bits/type_traits.h:243: error: previous definition of ` struct __type_traits' stl/type_traits.h:192: error: redefinition of `struct __type_traits<_Tp*>' /usr/include/c++/3.3/bits/type_traits.h:252: error: previous definition of ` struct __type_traits<_Tp*>' In file included from stl/alloc.h:21, from stl/deque.h:31, from FootPrinter.h:21, from merging.h:15, from merging.cc:15: stl/stl_alloc.h:677: warning: `__default_alloc_template::obj' is implicitly a typename stl/stl_alloc.h:677: warning: implicit typename is deprecated, please see the documentation for details In file included from stl/deque.h:32, from FootPrinter.h:21, from merging.h:15, from merging.cc:15: stl/stl_deque.h:739: warning: `deque::iterator' is implicitly a typename stl/stl_deque.h:739: warning: implicit typename is deprecated, please see the documentation for details In file included from stl/queue.h:35, from FootPrinter.h:22, from merging.h:15, from merging.cc:15: stl/stl_bvector.h:255:30: stl_vector.h: No such file or directory In file included from stl/list.h:32, from FootPrinter.h:23, from merging.h:15, from merging.cc:15: stl/stl_list.h:414: warning: `list::iterator' is implicitly a typename stl/stl_list.h:414: warning: implicit typename is deprecated, please see the documentation for details In file included from stl/stl_hashtable.h:41, from stl/hash_map.h:31, from FootPrinter.h:26, from merging.h:15, from merging.cc:15: stl/stl_tempbuf.h:62: warning: `iterator_traits::value_type' is implicitly a typename stl/stl_tempbuf.h:62: warning: implicit typename is deprecated, please see the documentation for details In file included from stl/hash_map.h:31, from FootPrinter.h:26, from merging.h:15, from merging.cc:15: stl/stl_hashtable.h: In member function `__hashtable_iterator hashtable::begin()': stl/stl_hashtable.h:262: warning: `vector<__hashtable_node*, Alloc>::iterator' is implicitly a typename stl/stl_hashtable.h:262: warning: implicit typename is deprecated, please see the documentation for details stl/stl_hashtable.h: In member function `__hashtable_iterator& __hashtable_iterator::operator++()': stl/stl_hashtable.h:537: warning: `vector<__hashtable_node*, Alloc>::iterator' is implicitly a typename stl/stl_hashtable.h:537: warning: implicit typename is deprecated, please see the documentation for details stl/stl_hashtable.h: In member function `void hashtable::clear()': stl/stl_hashtable.h:958: warning: `vector<__hashtable_node*, Alloc>::iterator' is implicitly a typename stl/stl_hashtable.h:958: warning: implicit typename is deprecated, please see the documentation for details make: *** [merging.o] Error 1 From Helge-Friedrich.Tippmann at alumni.TU-Berlin.DE Mon Sep 5 14:21:12 2005 From: Helge-Friedrich.Tippmann at alumni.TU-Berlin.DE (Helge Tippmann) Date: Mon, 5 Sep 2005 20:21:12 +0200 (CEST) Subject: [BiO BB] Re: BiO_Bulletin_Board Digest, Vol 11, Issue 2 In-Reply-To: <20050905160026.E54EB207F51@primary.bioinformatics.org> References: <20050905160026.E54EB207F51@primary.bioinformatics.org> Message-ID: <49767.80.163.51.11.1125944472.squirrel@mailbox.TU-Berlin.DE> Hej Christoph, would not mind to help. OSX (10.2.8) user. Where can we download the program? H > Send BiO_Bulletin_Board mailing list submissions to > bio_bulletin_board at bioinformatics.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > or, via email, send a message with subject or body 'help' to > bio_bulletin_board-request at bioinformatics.org > > You can reach the person managing the list at > bio_bulletin_board-owner at bioinformatics.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of BiO_Bulletin_Board digest..." > > > Today's Topics: > > 1. need software testing MacOSX and MS-WindowsME > (Dr. Christoph Gille) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 5 Sep 2005 10:50:26 +0200 (CEST) > From: "Dr. Christoph Gille" > Subject: [BiO BB] need software testing MacOSX and MS-WindowsME > To: BiO_Bulletin_Board at bioinformatics.org > Message-ID: > <51320.192.168.220.203.1125910226.squirrel at webmail.charite.de> > Content-Type: text/plain;charset=iso-8859-1 > > Dear All, > > If you are interested in protein sequences and structures and have some > spare minutes I would appreciate if you could test some system > dependent features of my software. > > It will not take long. > > Thanks Christoph > > > > > ------------------------------ > > _______________________________________________ > Bioinformatics.Org general forum - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > End of BiO_Bulletin_Board Digest, Vol 11, Issue 2 > ************************************************* > From golharam at umdnj.edu Mon Sep 12 00:23:44 2005 From: golharam at umdnj.edu (Ryan Golhar) Date: Mon, 12 Sep 2005 00:23:44 -0400 Subject: [BiO BB] a question about footprinter In-Reply-To: <431D3562.1050703@egeeninc.com> Message-ID: <03e501c5b751$c3e6bd40$d33d140a@GOLHARMOBILE1> Try emailing the authors. I remember having a similar problem, but don't remember the solution. I believe it was setting the version of GCC you have from GCC3 to GCC2 in the makefile: -#GCCVERSION = GCC3 -GCCVERSION = GCC2 +GCCVERSION = GCC3 +#GCCVERSION = GCC2 Ryan -- Ryan Golhar - golharam at umdnj.edu The Informatics Institute of UMDNJ -----Original Message----- From: bio_bulletin_board-bounces+golharam=umdnj.edu at bioinformatics.org [mailto:bio_bulletin_board-bounces+golharam=umdnj.edu at bioinformatics.org ] On Behalf Of Pavlos Pavlidis Sent: Tuesday, September 06, 2005 2:21 AM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] a question about footprinter Hi all, I have downloaded footprinter 2.0 for linux, and when I'm trying to install it, I get the following error message. I'm using debian. Thanks Pavlos pavlidis at metsis:~/FootPrinter2.0$ make g++ -O2 -I. -DSHORT_MOTIFS -c merging.cc In file included from /usr/include/c++/3.3/backward/iostream.h:31, from FootPrinter.h:19, from merging.h:15, from merging.cc:15: /usr/include/c++/3.3/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header. Please consider using one of the 32 headers found in section 17.4.1.2 of the C++ standard. Examples include substituting the header for the header for C++ includes, or instead of the deprecated header . To disable this warning use -Wno-deprecated. In file included from stl/iterator.h:36, from stl/algobase.h:33, from stl/deque.h:30, from FootPrinter.h:21, from merging.h:15, from merging.cc:15: stl/stl_iterator.h:249: warning: `iterator_traits::difference_type' is implicitly a typename stl/stl_iterator.h:249: warning: implicit typename is deprecated, please see the documentation for details stl/stl_iterator.h: In function `typename iterator_traits::difference_type __distance(InputIterator, InputIterator, input_iterator_tag)': stl/stl_iterator.h:250: warning: `iterator_traits::difference_type' is implicitly a typename stl/stl_iterator.h:250: warning: implicit typename is deprecated, please see the documentation for details stl/stl_iterator.h: At global scope: stl/stl_iterator.h:260: warning: `iterator_traits::difference_type' is implicitly a typename stl/stl_iterator.h:260: warning: implicit typename is deprecated, please see the documentation for details stl/stl_iterator.h:266: warning: `iterator_traits::difference_type' is implicitly a typename stl/stl_iterator.h:266: warning: implicit typename is deprecated, please see the documentation for details stl/stl_iterator.h:618: warning: `reverse_iterator::difference_type' is implicitly a typename stl/stl_iterator.h:618: warning: implicit typename is deprecated, please see the documentation for details In file included from stl/iterator.h:39, from stl/algobase.h:33, from stl/deque.h:30, from FootPrinter.h:21, from merging.h:15, from merging.cc:15: stl/type_traits.h:54: error: redefinition of `struct __true_type' /usr/include/c++/3.3/bits/type_traits.h:90: error: previous definition of ` struct __true_type' stl/type_traits.h:57: error: redefinition of `struct __false_type' /usr/include/c++/3.3/bits/type_traits.h:91: error: previous definition of ` struct __false_type' stl/type_traits.h:61: error: redefinition of `struct __type_traits<_Tp>' /usr/include/c++/3.3/bits/type_traits.h:94: error: previous definition of ` struct __type_traits<_Tp>' stl/type_traits.h:93: error: redefinition of `struct __type_traits' /usr/include/c++/3.3/bits/type_traits.h:131: error: previous definition of ` struct __type_traits' stl/type_traits.h:101: error: redefinition of `struct __type_traits' /usr/include/c++/3.3/bits/type_traits.h:139: error: previous definition of ` struct __type_traits' stl/type_traits.h:109: error: redefinition of `struct __type_traits' /usr/include/c++/3.3/bits/type_traits.h:147: error: previous definition of ` struct __type_traits' stl/type_traits.h:117: error: redefinition of `struct __type_traits' /usr/include/c++/3.3/bits/type_traits.h:163: error: previous definition of ` struct __type_traits' stl/type_traits.h:125: error: redefinition of `struct __type_traits' /usr/include/c++/3.3/bits/type_traits.h:171: error: previous definition of ` struct __type_traits' stl/type_traits.h:133: error: redefinition of `struct __type_traits' /usr/include/c++/3.3/bits/type_traits.h:179: error: previous definition of ` struct __type_traits' stl/type_traits.h:141: error: redefinition of `struct __type_traits' /usr/include/c++/3.3/bits/type_traits.h:187: error: previous definition of ` struct __type_traits' stl/type_traits.h:149: error: redefinition of `struct __type_traits' /usr/include/c++/3.3/bits/type_traits.h:195: error: previous definition of ` struct __type_traits' stl/type_traits.h:157: error: redefinition of `struct __type_traits' /usr/include/c++/3.3/bits/type_traits.h:203: error: previous definition of ` struct __type_traits' stl/type_traits.h:165: error: redefinition of `struct __type_traits' /usr/include/c++/3.3/bits/type_traits.h:227: error: previous definition of ` struct __type_traits' stl/type_traits.h:173: error: redefinition of `struct __type_traits' /usr/include/c++/3.3/bits/type_traits.h:235: error: previous definition of ` struct __type_traits' stl/type_traits.h:181: error: redefinition of `struct __type_traits' /usr/include/c++/3.3/bits/type_traits.h:243: error: previous definition of ` struct __type_traits' stl/type_traits.h:192: error: redefinition of `struct __type_traits<_Tp*>' /usr/include/c++/3.3/bits/type_traits.h:252: error: previous definition of ` struct __type_traits<_Tp*>' In file included from stl/alloc.h:21, from stl/deque.h:31, from FootPrinter.h:21, from merging.h:15, from merging.cc:15: stl/stl_alloc.h:677: warning: `__default_alloc_template::obj' is implicitly a typename stl/stl_alloc.h:677: warning: implicit typename is deprecated, please see the documentation for details In file included from stl/deque.h:32, from FootPrinter.h:21, from merging.h:15, from merging.cc:15: stl/stl_deque.h:739: warning: `deque::iterator' is implicitly a typename stl/stl_deque.h:739: warning: implicit typename is deprecated, please see the documentation for details In file included from stl/queue.h:35, from FootPrinter.h:22, from merging.h:15, from merging.cc:15: stl/stl_bvector.h:255:30: stl_vector.h: No such file or directory In file included from stl/list.h:32, from FootPrinter.h:23, from merging.h:15, from merging.cc:15: stl/stl_list.h:414: warning: `list::iterator' is implicitly a typename stl/stl_list.h:414: warning: implicit typename is deprecated, please see the documentation for details In file included from stl/stl_hashtable.h:41, from stl/hash_map.h:31, from FootPrinter.h:26, from merging.h:15, from merging.cc:15: stl/stl_tempbuf.h:62: warning: `iterator_traits::value_type' is implicitly a typename stl/stl_tempbuf.h:62: warning: implicit typename is deprecated, please see the documentation for details In file included from stl/hash_map.h:31, from FootPrinter.h:26, from merging.h:15, from merging.cc:15: stl/stl_hashtable.h: In member function `__hashtable_iterator hashtable::begin()': stl/stl_hashtable.h:262: warning: `vector<__hashtable_node*, Alloc>::iterator' is implicitly a typename stl/stl_hashtable.h:262: warning: implicit typename is deprecated, please see the documentation for details stl/stl_hashtable.h: In member function `__hashtable_iterator& __hashtable_iterator::operator++()': stl/stl_hashtable.h:537: warning: `vector<__hashtable_node*, Alloc>::iterator' is implicitly a typename stl/stl_hashtable.h:537: warning: implicit typename is deprecated, please see the documentation for details stl/stl_hashtable.h: In member function `void hashtable::clear()': stl/stl_hashtable.h:958: warning: `vector<__hashtable_node*, Alloc>::iterator' is implicitly a typename stl/stl_hashtable.h:958: warning: implicit typename is deprecated, please see the documentation for details make: *** [merging.o] Error 1 _______________________________________________ Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From ediths at unizh.ch Wed Sep 14 05:21:31 2005 From: ediths at unizh.ch (Edith Schlagenhauf) Date: Wed, 14 Sep 2005 11:21:31 +0200 Subject: [BiO BB] Sequence alignment to whole genome sequence Message-ID: Hi, what is/are the most appropriate tools/software to align hundreds of 700 bp sequences to a whole genome sequence (around 8Mb) of a closely related species/strain? TIA for your input, Edith ****************************************** Dr Edith Schlagenhauf Bioinformatics Institute of Plant Biology University of Zurich Zollikerstrasse 107 CH-8008 Zurich SWITZERLAND e-mail: ediths AT botinst DOT unizh DOT ch Tel.: +41 1 634 82 78 Fax : +41 1 634 82 04 ****************************************** From idoerg at burnham.org Fri Sep 16 15:56:01 2005 From: idoerg at burnham.org (Iddo Friedberg) Date: Fri, 16 Sep 2005 12:56:01 -0700 Subject: [BiO BB] Protein sequence clustering program needed Message-ID: <432B2351.2060702@burnham.org> I need a protein sequence clustering program for a relatively low sequence ID (30-40%), for a small (<=200) number of sequences. Ideas? Thanks, Iddo -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037 Tel: (858) 646 3100 x3516 Fax: (858) 713 9930 http://ffas.ljcrf.edu/~iddo From dmb at mrc-dunn.cam.ac.uk Fri Sep 16 17:34:23 2005 From: dmb at mrc-dunn.cam.ac.uk (dmb at mrc-dunn.cam.ac.uk) Date: Fri, 16 Sep 2005 22:34:23 +0100 (BST) Subject: [BiO BB] Protein sequence clustering program needed In-Reply-To: <432B2351.2060702@burnham.org> References: <432B2351.2060702@burnham.org> Message-ID: <33181.213.107.105.179.1126906463.squirrel@www.mrc-dunn.cam.ac.uk> > I need a protein sequence clustering program for a relatively low > sequence ID (30-40%), for a small (<=200) number of sequences. Ideas? blastclust is OK > Thanks, > > Iddo > > -- > > Iddo Friedberg, Ph.D. > The Burnham Institute > 10901 N. Torrey Pines Rd. > La Jolla, CA 92037 > Tel: (858) 646 3100 x3516 > Fax: (858) 713 9930 > http://ffas.ljcrf.edu/~iddo > > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From marty.gollery at gmail.com Fri Sep 16 18:37:38 2005 From: marty.gollery at gmail.com (Martin Gollery) Date: Fri, 16 Sep 2005 15:37:38 -0700 Subject: [BiO BB] Sequence alignment to whole genome sequence In-Reply-To: References: Message-ID: Hi Edith, I would recommend BLAT for this. Cheers, Marty On 9/14/05, Edith Schlagenhauf wrote: > > Hi, > > what is/are the most appropriate tools/software to align > hundreds of 700 bp sequences to a whole genome > sequence (around 8Mb) of a closely related species/strain? > > TIA for your input, > Edith > > > ****************************************** > Dr Edith Schlagenhauf > Bioinformatics > Institute of Plant Biology > University of Zurich > Zollikerstrasse 107 > CH-8008 Zurich > SWITZERLAND > > e-mail: ediths AT botinst DOT unizh DOT ch > Tel.: +41 1 634 82 78 > Fax : +41 1 634 82 04 > ****************************************** > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- -- Martin Gollery Associate Director Center For Bioinformatics University of Nevada at Reno Dept. of Biochemistry / MS330 775-784-7042 ----------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From gary at primary.bioinformatics.org Fri Sep 16 10:42:50 2005 From: gary at primary.bioinformatics.org (Gary Van Domselaar) Date: Fri, 16 Sep 2005 10:42:50 -0400 (EDT) Subject: [BiO BB] Sequence alignment to whole genome sequenc In-Reply-To: References: Message-ID: Hi Edith, If you are trying to align sequence reads to a to a reference genome, then NUCmer (part of MUMmer) would be appropriate. Regards, g. On Wed, 14 Sep 2005, Edith Schlagenhauf wrote: > Hi, > > what is/are the most appropriate tools/software to align > hundreds of 700 bp sequences to a whole genome > sequence (around 8Mb) of a closely related species/strain? > > TIA for your input, > Edith > > > ****************************************** > Dr Edith Schlagenhauf > Bioinformatics > Institute of Plant Biology > University of Zurich > Zollikerstrasse 107 > CH-8008 Zurich > SWITZERLAND > > e-mail: ediths AT botinst DOT unizh DOT ch > Tel.: +41 1 634 82 78 > Fax : +41 1 634 82 04 > ****************************************** > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- Gary Van Domselaar, PhD Associate Director, Bioinformatics.Org gary at bioinformatics.org From shivamsrivastava at gmail.com Sat Sep 17 13:30:34 2005 From: shivamsrivastava at gmail.com (shivam srivastava) Date: Sat, 17 Sep 2005 23:00:34 +0530 Subject: [BiO BB] help! Message-ID: <1cfc45350509171030147b034a@mail.gmail.com> Hi! I'm into a short project (domain problem). To find out unique conserved region among conserved regions of genomes in evolution right from very primitive species to highly advanced species using internet & public databases as the working platform The results would include >DNA seq. of Unique conserved region & protein seq if available >SNPs identified in the unique conserved region What"ll be the likely approach to this problem with respect to the tools . Should i go for similarity search or identity? multiple or global alignment & which level of genome (transcriptome/mRNA) should i work with? I'll be highly thankful for ur guidance -------------- next part -------------- An HTML attachment was scrubbed... URL: From veredcc at bgumail.bgu.ac.il Sun Sep 18 02:34:24 2005 From: veredcc at bgumail.bgu.ac.il (Vered Caspi) Date: Sun, 18 Sep 2005 09:34:24 +0300 Subject: [BiO BB] Protein sequence clustering program needed References: <432B2351.2060702@burnham.org> Message-ID: <005901c5bc1b$02b71920$32594884@veredcc> Iddo, We are using a local installation of MKDOM for protein clustering (to the level of conserved domains). Vered ______________________________________________________________ Vered Caspi, Ph.D. Bioinformatics Support Unit, Head National Institute for Biotechnology in the Negev Building 39, room 214 Ben-Gurion University of the Negev Beer-Sheva 84105, Israel Email: veredcc at bgumail.bgu.ac.il Tel: 08-6479034 054-7915969 Fax: 08-6472983 http://bioinfo.bgu.ac.il ______________________________________________________________ ----- Original Message ----- From: "Iddo Friedberg" To: "The general forum at Bioinformatics.Org" Sent: Friday, September 16, 2005 10:56 PM Subject: [BiO BB] Protein sequence clustering program needed I need a protein sequence clustering program for a relatively low sequence ID (30-40%), for a small (<=200) number of sequences. Ideas? Thanks, Iddo -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037 Tel: (858) 646 3100 x3516 Fax: (858) 713 9930 http://ffas.ljcrf.edu/~iddo _______________________________________________ Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From stefanielager at fastmail.ca Mon Sep 19 02:13:41 2005 From: stefanielager at fastmail.ca (Stefanie Lager) Date: Mon, 19 Sep 2005 06:13:41 +0000 (UTC) Subject: [BiO BB] Protein sequence clustering program needed In-Reply-To: <432B2351.2060702@burnham.org> Message-ID: <20050919061343.B3693861450@mail.interchange.ca> CD-HIT is probably the most commonly used clustering program http://bioinformatics.ljcrf.edu/cd-hi/ Stefanie > I need a protein sequence clustering program for a relatively low > sequence ID (30-40%), for a small (<=200) number of sequences. Ideas? > > Thanks, > > Iddo > > -- > > Iddo Friedberg, Ph.D. > The Burnham Institute > 10901 N. Torrey Pines Rd. > La Jolla, CA 92037 > Tel: (858) 646 3100 x3516 > Fax: (858) 713 9930 > http://ffas.ljcrf.edu/~iddo > > _______________________________________________ > Bioinformatics.Org general forum - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board _________________________________________________________________ http://fastmail.ca/ - Fast Secure Web Email for Canadians From stefanielager at fastmail.ca Mon Sep 19 02:17:44 2005 From: stefanielager at fastmail.ca (Stefanie Lager) Date: Mon, 19 Sep 2005 06:17:44 +0000 (UTC) Subject: [BiO BB] Sequence alignment to whole genome sequence In-Reply-To: Message-ID: <20050919061745.3F0398613FD@mail.interchange.ca> Software for EST/cDNA to genome alignment might work. Wu TD, Watanabe CK. GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics. 2005 May 1;21(9):1859-75. Epub 2005 Feb 22. Slater GS, Birney E. Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics. 2005 Feb 15;6(1):31. > Hi, > > what is/are the most appropriate tools/software to align > hundreds of 700 bp sequences to a whole genome > sequence (around 8Mb) of a closely related species/strain? > > TIA for your input, > Edith > > > ****************************************** > Dr Edith Schlagenhauf > Bioinformatics > Institute of Plant Biology > University of Zurich > Zollikerstrasse 107 > CH-8008 Zurich > SWITZERLAND > > e-mail: ediths AT botinst DOT unizh DOT ch > Tel.: +41 1 634 82 78 > Fax : +41 1 634 82 04 > ****************************************** > _______________________________________________ > Bioinformatics.Org general forum - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board _________________________________________________________________ http://fastmail.ca/ - Fast Secure Web Email for Canadians From bioinfosm at gmail.com Mon Sep 19 12:08:07 2005 From: bioinfosm at gmail.com (Samantha Fox) Date: Mon, 19 Sep 2005 11:08:07 -0500 Subject: [BiO BB] Transfac doubt Message-ID: <72645081050919090811bcd996@mail.gmail.com> Hi, I am using the TRANSFAC Professional 9.2 for my analysis. I had a couple of questions. Match works fine with a small sequence set. However when I use a big dataset, it runs and displays no output. I checked in the tmp files, and there was a file with results, but just does not get displayed. Can you help me on this? Also is there a way I can run it in batch mode ? Secondly is there a way to get all possible transfac matrices that I can use ? Thanks ! -------------- next part -------------- An HTML attachment was scrubbed... URL: From gary at primary.bioinformatics.org Tue Sep 20 12:09:30 2005 From: gary at primary.bioinformatics.org (Gary Van Domselaar) Date: Tue, 20 Sep 2005 12:09:30 -0400 (EDT) Subject: [BiO BB] Recommendations for Sequence Profile Conservation Plotting Software In-Reply-To: References: Message-ID: Hey Gang, Im wondering what software is out there for generating plots of the degree of sequence conservation from (possibly supplied) multiple alignments at t 2000+ bp scale. I'm aware of eShadow and I guess Sockeye, but Im wondering if there is anything else as good or better. Kindest Regards, g. -- Gary Van Domselaar, PhD Associate Director, Bioinformatics.Org gary at bioinformatics.org From announcements at virtualgenomics.org Thu Sep 22 04:05:34 2005 From: announcements at virtualgenomics.org (announcements at virtualgenomics.org) Date: Thu, 22 Sep 2005 01:05:34 -0700 Subject: [BiO BB] Fifth Virtual Conference on Genomics and Bioinformatics Message-ID: <20050922010534.d30baca04aa409132ad42be930eb52b5.bea231a6ae.wbe@email.email.secureserver.net> Fifth Virtual Conference on Genomics and Bioinformatics October 25-28, 2005 Sharing Knowledge with the World The Virtual Conference central broadcasting location is The Alliance Center for Collaboration, Education, Science and Software (ACCESS). >From this location several speakers will be presenting their research... This site will host a maximum of 150 researchers and students. No registration fees http://www.virtualgenomics.org/vcgb/conference_2005.htm The virtual conference on genomics and bioinformatics (V-VCGB) is an advanced collaborative environment featuring top researchers involved in the fields of Computational Biology, Structural Genomics, Toxicogenomics and Cancer Research, Databases, Infectious Diseases, Ethics and Education and Nanobiotechnology. The main objectives of the Virtual Conference are: * Transcend geographical and economical barriers for the exchange of ideas that facilitates the interaction and collaboration among scientists and educators around the world. * Address the benefits and limitations of the newest developments in post-genomic technologies. * Explore the social and ethical implications of genomic and bioinformatic research. * Establish new ways to introduce the high school community to today's multidisciplinary science. In order to accomplish our objectives, the Virtual Conference on Genomics and Bioinformatics is completed without registration fees. The conference is broadcast around the world using Access Grid and real-time video streaming technologies. In addition to the real-time virtual conference, presentations (visual and audio) are available on the web for delayed streaming. Threaded discussion sessions with the invited speakers and additional peer-reviewed paper sessions follow the conference. Who Should Attend? Students, Bioinformatics' project leaders, Statisticians, Artificial and Synthetic Life, Computational Biologists, Computational Chemists, IT leaders and Genomic database administrators, Biotechnology business analysts and anyone involved in the analysis of the genomic structure and dynamics of living systems To register to one of the Virtual Sites around the world: http://www.virtualgenomics.org/vcgb/registration.php To check the program: http://www.virtualgenomics.org/vcgb/program_2005.htm From mayagao1999 at yahoo.com Fri Sep 23 00:15:18 2005 From: mayagao1999 at yahoo.com (Alex Zhang) Date: Thu, 22 Sep 2005 21:15:18 -0700 (PDT) Subject: [BiO BB] Seek advice on programming of miRNA problem Message-ID: <20050923041518.4318.qmail@web53503.mail.yahoo.com> Dear all, I am doing something about miRNA mapping. Please suggest me on this question. Thank you very much ahead of time. Sincerely, Alex Basically, 1. There are two files to be processed. The first one is ?HuBACmap_OG1_4x4_Bld35v1_Mar8-05? which contains the array information about Bacteria Artificial Chromosomes. The other one is called ?miRNA maps? which holds the information about the microRNAs gained from UCSC Genome Center. 2. ?HuBACmap_OG1_4x4_Bld35v1_Mar8-05? file holds 8 columns and 9575 rows. The first row looks like: ID Block Column Row Chrom Start End Mid >From the 2nd row to the last row, the information about each BAC is listed block by block (there are 16 blocks from Block 1 to Block 16). A snapshot would be like: RP11-125P20 1 18 1 01 88031403 88194307 88112855 RP11-72M14 1 19 1 01 112869186 112904105 112886645 RP11-130B18 1 20 1 NA NA NA RP11-192J8 1 21 1 01 118214732 118215022 118214877 The features for this file are: (1) The important information which will be used are: ?ID? which identify the individual BAC on each chromosome. ?Chrom? which stands for each chromosome. There are 23 chromosomes. ?Start? and ?End? which specify the location of each BAC on each chromosome. (2) This file includes some unknown information which is designated by ?NA?. If in this case, the row including ?NA? should be ignored. (3) There are duplicate data for some BACs. For example, you may find: RP11-192J8 1 21 1 01 118214732 118215022 118214877 RP11-192J8 2 45 1 01 118214732 118215022 118214877 Which means that these two rows hold the same information at least for ID, Chrom, Start, End and Mid even though the values for Block or Column are different. If in this case, the program should be able to recognize the duplicate information and pick any row for further processing. (4) The length of the site which each BAC occupies ranges from 100bps-350bps. 3. ?miRNA maps? file holds 10 columns and 325 rows. The first row looks like: #bin chrom chromStart chromEnd name score strand thickStart thickEnd type >From the 2nd row to the last row, the information about each microRNA is listed chromosome by chromosome (there are 23 chromosomes from Ch 1 to Ch X). A snapshot would be like: 593 chr1 1142406 1142501 hsa-mir-200b 960 + 1142459 1142483 miRna 593 chr1 1143165 1143255 hsa-mir-200a 960 + 1143180 1143202 miRna The features for this file are: (1) The important information which will be used are: ?chrom? which identify the chromosome occupied by microRNA. ?name? which is the unique name for each microRNA. ?thickStart? and ?thickEnd? specify the site which microRNA occupies. (2) Usually the length for each site is around 22. 4. The task is to identify on each chromosome the flanking BACs for each microRNA and which one is much closer to the microRNA. To make it easy to understand, we use a figure to illustrate: _________________* miRNA *_____________________________________ *BAC0* * BAC1*___| |____________* BAC2 * * BAC3 * D1 D2 Note: "*" defines the boundary for miRNA or BAC. BAC1 is one of the flanking BACs for miRNA because it is much closer than BAC0; BAC2 is another flanking BAC for miRNA because it is much closer than BAC3; After determining the sites of flanking BACs, we will calculate the distance between each flanking BAC and miRNA, which will be D1 and D2. If D1 is greater than D2, we could say BAC2 is much closer to miRNA than BAC1. Then we will end up with a list like: Chrom name ID1 ID2 ID3 D1 D2 thickStart thickEnd ?Chrom? for each chromosome; ?name? for each miRNA; ?ID1? for the left flanking BAC for each miRNA; ?ID2? for the right flanking BAC for each each miRNA; ?ID3? for the flanking BAC which is closer to miRNA; ?D1? for the distance between the left flanking BAC and miRNA; ?D2? for the distance between the right flanking BAC and miRNA; ?thickStart? and ?thickEnd? specify the site which microRNA occupies 5. We also can imagine some special cases which might exist. For example, there is a possiblity that a miRNA shares a common region with its flanking BAC,which looks like: _________________* miRNA *____________________ * BAC * It is simple to say that this BAC is a flanking one for this miRNA. Besides, there is another possibilty that a miRNA is within a BAC, which looks like: _________________* miRNA *____________________ * BAC * This may happen because the length for a miRNA is around 22 and the length for a BAC is more than 100. If in this case, we will suggest that this miRNA has only one BAC and the distance is 0. For example, Chrom name ID1 ID2 ID3 D1 D2 thickStart thickEnd 1 hsa-mir-200 RP12 RP12 RP12 0 0 116677 116699 ______________________________________________________ Yahoo! for Good Donate to the Hurricane Katrina relief effort. http://store.yahoo.com/redcross-donate3/ From jyoti_bioinfo at rediffmail.com Mon Sep 26 01:57:17 2005 From: jyoti_bioinfo at rediffmail.com (Jyoti ) Date: 26 Sep 2005 05:57:17 -0000 Subject: [BiO BB] seeking advice for finding multidomain proteins Message-ID: <20050926055717.10729.qmail@webmail43.rediffmail.com> Hi, Plz suggest me a program or algorithm or any appropriate method for finding a multidomain proteins in the whole genome of Mycobacterium tuberculosis. Thanx Jyoti Jyoti -------------- next part -------------- An HTML attachment was scrubbed... URL: From dmb at mrc-dunn.cam.ac.uk Mon Sep 26 03:16:16 2005 From: dmb at mrc-dunn.cam.ac.uk (dmb at mrc-dunn.cam.ac.uk) Date: Mon, 26 Sep 2005 08:16:16 +0100 (BST) Subject: [BiO BB] seeking advice for finding multidomain proteins In-Reply-To: <20050926055717.10729.qmail@webmail43.rediffmail.com> References: <20050926055717.10729.qmail@webmail43.rediffmail.com> Message-ID: <33220.213.107.105.179.1127718976.squirrel@www.mrc-dunn.cam.ac.uk> > > Hi, > > Plz suggest me a program or algorithm or any appropriate method for > finding a multidomain proteins in the whole genome of Mycobacterium > tuberculosis. DIVCLUS: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9545446&query_hl=1 > Thanx > > Jyoti > > Jyoti_______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From adarshramakumar at yahoo.co.uk Mon Sep 26 03:44:33 2005 From: adarshramakumar at yahoo.co.uk (Adarsh Ramakumar) Date: Mon, 26 Sep 2005 08:44:33 +0100 (BST) Subject: [BiO BB] seeking advice for finding multidomain proteins In-Reply-To: <33220.213.107.105.179.1127718976.squirrel@www.mrc-dunn.cam.ac.uk> Message-ID: <20050926074433.24587.qmail@web25503.mail.ukl.yahoo.com> Hi There are many programs: Pfam(HMMER),SMART,Prodom,CDD(NCBI).... Just search in google and you will find lots.... cheers --- dmb at mrc-dunn.cam.ac.uk wrote: > > > > Hi, > > > > Plz suggest me a program or algorithm or any > appropriate method for > > finding a multidomain proteins in the whole genome > of Mycobacterium > > tuberculosis. > > DIVCLUS: > http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9545446&query_hl=1 > > > > Thanx > > > > Jyoti > > > > > Jyoti_______________________________________________ > > Bioinformatics.Org general forum - > BiO_Bulletin_Board at bioinformatics.org > > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > > _______________________________________________ > Bioinformatics.Org general forum - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > Mr. Adarsh Ramakumar, BioInformatics, University of Bremen. http://www.biox.uni-bremen.de Mail: adarshbiox at uni-bremen.de Tel (W) +49-421-2182911. Mobile +49-1747273680. ___________________________________________________________ Yahoo! Messenger - NEW crystal clear PC to PC calling worldwide with voicemail http://uk.messenger.yahoo.com From elavv2003 at gmail.com Tue Sep 27 01:26:59 2005 From: elavv2003 at gmail.com (Elavazhagan) Date: Tue, 27 Sep 2005 10:56:59 +0530 Subject: [BiO BB] research articles Message-ID: Hai, Let me except some ideas that how do we implement our coding as well as molecular modeling knowledge to make as research proposal for the following topics. Identification of co-occurring transcription factor binding sites in co-regulated genes, Computational detection and analysis of miRNA targets. Thanking You -------------- next part -------------- An HTML attachment was scrubbed... URL: From smagarwal at yahoo.com Tue Sep 27 05:32:48 2005 From: smagarwal at yahoo.com (Subhash Agarwal) Date: Tue, 27 Sep 2005 10:32:48 +0100 (BST) Subject: [BiO BB] Placing ligand in a modeled protein Message-ID: <20050927093248.37748.qmail@web31510.mail.mud.yahoo.com> Hi I would like to know how can i place ligand in modelled protein. I have a template with ligand in it which i need to transfer to already built model. Thanking You With regards Subhash __________________________________________________________ Yahoo! India Matrimony: Find your partner now. Go to http://yahoo.shaadi.com From fidel.ramirez at mpi-inf.mpg.de Tue Sep 27 08:24:54 2005 From: fidel.ramirez at mpi-inf.mpg.de (=?ISO-8859-1?Q?Fidel_Ram=EDrez?=) Date: Tue, 27 Sep 2005 14:24:54 +0200 Subject: [BiO BB] Placing ligand in a modeled protein In-Reply-To: <20050927093248.37748.qmail@web31510.mail.mud.yahoo.com> References: <20050927093248.37748.qmail@web31510.mail.mud.yahoo.com> Message-ID: <0645e90be7a9b97482d441e08749a96e@mpi-inf.mpg.de> I'm not specialist in the field, but have you tried FlexX ? On 27/09/2005, at 11:32, Subhash Agarwal wrote: > Hi > > I would like to know how can i place ligand in > modelled protein. I have a template with ligand in it > which i need to transfer to already built model. > > Thanking You > > With regards > Subhash > > > > > > __________________________________________________________ > Yahoo! India Matrimony: Find your partner now. Go to > http://yahoo.shaadi.com > _______________________________________________ > Bioinformatics.Org general forum - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > Fidel Ram?rez +49 (0)681 9325 321 Max-Planck-Institute for Informatics, Department of Bioinformatics Stuhlsatzenhausweg 85 66123 Saarbruecken GERMANY Fidel Ram?rez +49 (0)681 9325 321 Max-Planck-Institute for Informatics, Department of Bioinformatics Stuhlsatzenhausweg 85 66123 Saarbruecken GERMANY From joel.dudley at asu.edu Wed Sep 28 04:38:05 2005 From: joel.dudley at asu.edu (Joel Dudley) Date: Wed, 28 Sep 2005 01:38:05 -0700 Subject: [BiO BB] Announcing MacResearcher.com Message-ID: <6820E6B9-67C1-4E74-A130-2A13392D31AD@asu.edu> The MacResearcher team is proud to announce the official launch of MacResearcher.com (http://www.macresearcher.com), the ultimate online resource and community for the Mac-loving scientist. MacResearcher offers articles, news, and reviews as well as a diverse selection of forums for community interaction. In the true spirit of community MacResearcher allows and encourages all members to step up to the digital soap box and submit content for publication on the MacResearcher.com main page. If your an Xgrid guru, a digital gene hacker, algorithm architect, or Powerbook toting physicist, MacResearcher offers you the platform to share your arcane knowledge with the ?ber-intelligent world of MacResearchers. MacResearcher.com is for MacResearchers by MacResearchers, so If you'd like to add a feature to the site, run a MacResearcher blog, or host an open-source software project, MacResearcher can accommodate you. Head over to http://www.macresearcher.com now for the latest news, tips, and tricks. All forms of feedback are welcome. Thank you for taking the time to read our announcement. Sincerely, MacResearcher.com Team From Reactome-Knowledgebase at reactome.org Mon Sep 26 18:09:18 2005 From: Reactome-Knowledgebase at reactome.org (Reactome-Knowledgebase at reactome.org) Date: Mon, 26 Sep 2005 18:09:18 -0400 Subject: [BiO BB] Reactome - Ver 15 released! Message-ID: The Reactome Knowledgebase group (Cold Spring Harbor Lab and the European Bioinformatics Institute) is proud to announce the release of Reactome Version 15 today, accessible at http://www.reactome.org . Reactome is a curated knowledgebase of biological processes in humans. It covers processes ranging from basic pathways of metabolism to complex events such as hormonal signaling and apoptosis. The information in Reactome is provided by expert bench biologists, and edited and managed as a relational database by the Reactome staff. New material is peer-reviewed and revised as necessary before publication to the web. Reactome version 15 features: - a new module on the integration of energy metabolism, bringing the total number of curated reactions in the knowledgebase to 1463 and the total number of annotated human proteins to 1095; [that's the number of reference UniProt protein entities - would be 1525 if we counted each modified form of a protein as a separate entity] - a revised data model improves the handling of physical entities (molecules and complexes) and introduces the concept of an entity set to allow the explicit annotation of functions shared by a family of molecules such as protein isoforms; - a new strategy for electronic inference of events in model organisms from curated human reactions that uses OrthoMCL to identify the human : model organism protein orthologies for event inference. The sensitivity of OrthoMCL has enabled the inference of event sets for organisms ranging from the laboratory mouse (inferences made for 1368 of 1463 human reactions, a 93.5% success rate) to the archaebacterium Methanococcus jannaschii (185 events, 12.6% success). - new web features for display of event hierarchies and the components of individual reactions, and an on-line editorial calendar, linked to the Reactome home page, that summarizes work in progress on new modules for the knowledgebase. Links from and to Reactome are available for corresponding entries in NCBI Entrez Gene, Protein, OMIM, Ensembl genome annotations, UCSC Genome Browser, KEGG, ChEBI and Gene Ontology databases. Questions or comments? Reply to this email or please send e-mail to help at reactome.org. - Reactome Group at CSHL and EBI www.reactome.org