From mike.fursov at gmail.com Mon Aug 1 01:19:28 2011 From: mike.fursov at gmail.com (Mikhail Fursov) Date: Mon, 1 Aug 2011 12:19:28 +0700 Subject: [BiO BB] Running BLAST with a new scoring matrix In-Reply-To: References: Message-ID: I know that this can easily be done with Smith Waterman algorithm: more precise but slow in comparison with BLAST. To check your matrix with Smith Waterman you can download UGENE tool ( http://ugene.unipro.ru ), open the sequence you want to analyze and select "Actions->Analyze->Smith-Waterman" menu. There you will see an option to select a custom scoring matrix. On Fri, Jul 29, 2011 at 11:10 AM, Dr. Achuthsankar S. Nair wrote: > Hi > I have developed a new scoring matrix to replace PAM, can anyone suggest how > we can test this out in alignment tools inclusing BLAST ? > Is there a tool which accepts user defined ?scoring matrix ? > Thanks in advance > Achu > > -- > > Dr Achuthsankar S Nair > Director, State Inter-University ?Centre for Bioinformatics > University of Kerala, Trivandrum 695581, INDIA > Tel (O) 471-2308759 (R) 471-2542220 > www.cbi.keralauniversity.edu > www.achu.keralauniversity.edu > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > From Alex.Bossers at wur.nl Mon Aug 1 16:44:29 2011 From: Alex.Bossers at wur.nl (Bossers, Alex) Date: Mon, 1 Aug 2011 22:44:29 +0200 Subject: [BiO BB] Running BLAST with a new scoring matrix In-Reply-To: References: Message-ID: <605CF62A79C32E4AA0CC741FD84D4E7426689349DB@scomp0536.wurnet.nl> Achu, Have a look at the NCBI blast+ documentation (snippet below). It will allow what you want I guess; The -matrix option. Alex $ blastx -help USAGE blastx [-h] [-help] [-import_search_strategy filename] [-export_search_strategy filename] [-db database_name] [-dbsize num_letters] [-gilist filename] [-seqidlist filename] [-negative_gilist filename] [-entrez_query entrez_query] [-db_soft_mask filtering_algorithm] [-db_hard_mask filtering_algorithm] [-subject subject_input_file] [-subject_loc range] [-query input_file] [-out output_file] [-evalue evalue] [-word_size int_value] [-gapopen open_penalty] [-gapextend extend_penalty] [-xdrop_ungap float_value] [-xdrop_gap float_value] [-xdrop_gap_final float_value] [-searchsp int_value] [-frame_shift_penalty frameshift] [-max_intron_length length] [-seg SEG_options] [-soft_masking soft_masking] [-matrix matrix_name] [-threshold float_value] [-culling_limit int_value] [-best_hit_overhang float_value] [-best_hit_score_edge float_value] [-window_size int_value] [-ungapped] [-lcase_masking] [-query_loc range] [-strand strand] [-parse_deflines] [-query_gencode int_value] [-outfmt format] [-show_gis] [-num_descriptions int_value] [-num_alignments int_value] [-html] [-max_target_seqs num_sequences] [-num_threads int_value] [-remote] [-version] DESCRIPTION Translated Query-Protein Subject BLAST 2.2.25+ Use '-help' to print detailed descriptions of command line arguments ---------------------- THis should do it: -matrix Scoring matrix name (normally BLOSUM62) ======================== ________________________________________ Van: bbb-bounces at bioinformatics.org [bbb-bounces at bioinformatics.org] namens Dr. Achuthsankar S. Nair [sankar.achuth at gmail.com] Verzonden: vrijdag 29 juli 2011 6:10 Aan: bbb at bioinformatics.org Onderwerp: [BiO BB] Running BLAST with a new scoring matrix Hi I have developed a new scoring matrix to replace PAM, can anyone suggest how we can test this out in alignment tools inclusing BLAST ? Is there a tool which accepts user defined scoring matrix ? Thanks in advance Achu -- Dr Achuthsankar S Nair Director, State Inter-University Centre for Bioinformatics University of Kerala, Trivandrum 695581, INDIA Tel (O) 471-2308759 (R) 471-2542220 www.cbi.keralauniversity.edu www.achu.keralauniversity.edu _______________________________________________ BBB mailing list BBB at bioinformatics.org http://www.bioinformatics.org/mailman/listinfo/bbb From barry.hardy at vtxmail.ch Wed Aug 3 06:27:34 2011 From: barry.hardy at vtxmail.ch (Barry Hardy) Date: Wed, 03 Aug 2011 12:27:34 +0200 Subject: [BiO BB] OpenTox Meeting: Innovation in Predictive Toxicology, Munich Message-ID: <4E392296.8070800@vtxmail.ch> We can accommodate a couple of last minute registrations for the OpenTox workshop and meeting activity in Munich next week: http://www.opentox.org/meet/opentox2011 There is no registration fee to participate but we do need to have confirmed attendance. If you are interested in joining, please contact me with your details. Thanks! best regards Barry Hardy (Douglas Connect) and Stefan Kramer (Technical University of Munich) OpenTox InterAction Meeting Co-Chairs Barry Hardy PhD Director, Community of Practice & Research Activities and OpenTox Project Coordinator (www.opentox.org) Douglas Connect Baermeggenweg 14 4314 Zeiningen Switzerland From mazumder at email.gwu.edu Wed Aug 3 07:45:22 2011 From: mazumder at email.gwu.edu (Raja Mazumder) Date: Wed, 03 Aug 2011 07:45:22 -0400 Subject: [BiO BB] Call for papers: 5th International Biocuration Conference Washington DC (submission deadline: October 15, 2011) Message-ID: <4E3934D2.1000305@email.gwu.edu> Dear colleagues, The International Biocuration Conference is a unique event for curators and developers of biological databases to discuss their work, promote collaborations, and foster a sense of community in this very active and growing area of research. In preparation for the 5th International Biocuration Conference (http://pir.georgetown.edu/biocuration2012.html) (April 2-4, 2012; Washington DC), we invite you to submit your work to be considered for publication in a special issue of Database: The Journal of Biological Databases and Curation (http://database.oxfordjournals.org/). Additionally your work will be considered for an oral presentation at the Biocuration 2012 meeting. This is a great opportunity to enhance the recognition of our profession by the greater biological research communities. Submitters are welcomed to select amongst topics of the seven sessions in Biocuration 2012: 1. Ontologies, standards and best practices, including gold standard datasets. 2. Protein annotation; sequences, structures and pathways. 3. Community annotation and Wikis. 4. Genomics and metagenomics data curation. 5. HTP data (focus on NGS and MS data) curation and presentation. 6. Literature collection, text mining and curation. 7. Tools to assist curation, including automated pipelines. Accepted papers will be given special consideration by the Biocuration 2012 session chairs for selection as oral presentations. In the event that an accepted paper does not fit the scope of any of the session topics, the paper will still be considered for publication in DATABASE, although it may not be invited for an oral presentation at the conference. The Journal DATABASE will create a virtual issue with papers from the Biocuration Conference in Washington DC on April 2-4, 2012. This virtual issue will be printed and distributed to conference attendees. Because of this, the review process for these papers will be expedited, making the following submission deadlines non-negotiable: ? Call for papers: August 1, 2011 ? Submission deadline: October 15, 2011 ? First decisions: November 15, 2011 ? Deadline for revisions: December 15, 2011 ? Final decisions: January 10, 2012 ? Conference: April 2-4 2012 Authors wishing to submit to DATABASE for the 2012 BIOCURATION VIRTUAL ISSUE should go to the DATABASE home page (http://database.oxfordjournals.org/) and follow the guidelines on the "Instructions to Authors" section. When ready, authors will start the process of submission by following the link "Submit Now!". All authors must CLEARLY state for the staff at DATABASE that they are submitting this manuscript for consideration for the 2012 Annual Biocuration Conference. This way their staff may ensure appropriate fast-track options for inclusion in the proceedings of this meeting. Finally, when filling the DATABASE submission form, authors MUST select "Biocuration Conference Paper" as their manuscript type: We look forward to your participation at the 5th International Biocuration Conference. Kind regards, - The Biocuration 2012 Organizing Committee. From s_uchida21 at yahoo.co.jp Wed Aug 3 23:17:45 2011 From: s_uchida21 at yahoo.co.jp (=?iso-2022-jp?B?GyRCRmJFRBsoQiAbJEJMdzpIGyhC?=) Date: Thu, 4 Aug 2011 12:17:45 +0900 (JST) Subject: [BiO BB] extracting highly expressed and low expressed genes from any database/ plasmodb. In-Reply-To: Message-ID: <113869.62710.qm@web3114.mail.ogk.yahoo.co.jp> Dear Manoj: Hello. Try our knowledge database called "C-It" (http://C-It.mpi-bn.mpg.de). You can find the description about it here: http://bioinformatics.oxfordjournals.org/content/26/18/2328.abstract Shizuka --- On Mon, 2011/8/1, Manoj Yadav wrote: hello to all users, Please give some suggestions regarding the extraction of highly expressed and low expressed genes from any database/ plasmodb. I am really messed up in this situation. Plz help me. thanks in advance. -- * ------ With Regards ------- Manoj Kumar Yadav* Research Scholar, Bioinformatics Program MMV, BHU,Varanasi +91 8004356248 "Until you spread your wings, you'll have no idea how far you can fly" _______________________________________________ BBB mailing list BBB at bioinformatics.org http://www.bioinformatics.org/mailman/listinfo/bbb From Phoebe.Chen at latrobe.edu.au Fri Aug 5 10:01:47 2011 From: Phoebe.Chen at latrobe.edu.au (Phoebe Chen) Date: Sat, 6 Aug 2011 00:01:47 +1000 Subject: [BiO BB] CFP - APBC2012 - 10 days left Message-ID: Dear Colleague, ============================================================== Full paper submission deadline is due on August 15, 2011. (10 days left) *Please send to interested colleagues and students * Deadline Extended: APBC2012 - The Tenth Asia Pacific Bioinformatics Conference The Tenth Asia Pacific Bioinformatics Conference Melbourne, Australia, 17-19 January 2012 http://homepage.cs.latrobe.edu.au/ypchen/APBC2012/ ============================================================== Important Dates Extended Paper submission: 15th August 2011 ****** Author Notification: 20th Sep 2011 Final Version due on: 10th Oct 2011 Tutorial submission open: 1st July 2011 Poster submission open: 3rd Oct 2011 Registration open: 22nd Aug 2011 The Asia-Pacific Bioinformatics Conference series is an annual forum for exploring research, development and novel applications of Bioinformatics. The past APBC conferences were held in: *APBC2003 4-7 Feb 2003: Adelaide Australia *APBC2004 18-22 Jan 2004: Dunedin, New Zealand *APBC2005 17-21 Jan 2005: Singapore *APBC2006 13-16 Feb, 2006: Taipei Taiwan *APBC2007 15-17 Jan, 2007: Hong Kong *APBC2008 14-17 Jan, 2008: Kyoto Japan *APBC2009 13-16 Jan, 2009: Beijing China *APBC2010 18-21 Jan, 2010: Bangalore, India *APBC2011 11-14 Jan, 2011: Inchon, Korea The past APBC papers: http://homepage.cs.latrobe.edu.au/ypchen/APBChomepage.htm Topics of Interest Papers are solicited on, but not limited to, the following topics: - Sequence Analysis - Motif Finding - Ontology - Databases and Data Integration - Biomedical Literature Mining and Understanding - Recognition of Genes and Functional Elements - RNA Analysis - Physical and Genetic Mapping - Molecular Evolution and Phylogeny - Protein Structure Analysis - Microarray Design and Data Analysis - Deep Sequencing Data Processing - Transcriptome, Gene Expression - Epigenomics - Proteomics and Post-Translational Modifications - Pathways, Networks and Systems - Population Genetics, SNP and Haplotyping - Comparative Genomics ----------------------------------------------------------------------------------------------------------------------- Call for Papers APBC2012 invites high-quality original full papers on any topic related to Bioinformatics and Computational Biology. The submitted papers must have not been published or under consideration for publication in any other journal or conference with formal proceedings. All accepted papers will have to be presented by one of the authors at the conference. All accepted papers will be invited to be published in the journal BMC Genomics, Proteomics, IEEE/ACM Transactions on Computational Biology and Bioinformatics, International Journal of Bioinformatics Research and Applications. Papers should be 30 pages (1 column) 12 point font, including the title, authors and addresses, abstract, text, figures, tables, and references, please follow the style according to. TeX/LaTeX - TeX template, http://www.biomedcentral.com/info/ifora/tex Microsoft Word - Word template, http://www.biomedcentral.com/download/templates/BMC154d.dot Authors can provide supplementary materials at their own website if necessary. Use the following linked site to make your submission https://www.easychair.org/account/signin.cgi?conf=apbc2012 Program Committee Chairs: Peer Bork, EMBL Heidelberg, Germany Phoebe Chen, La Trobe University, Australia Program Committee Members (Confirmed): Tatsuya Akutsu, Kyoto University, Japan Masanori Arita, University of Tokyo, Japan Joel Bader, Johns Hopkins University, USA Vladimir Brusic, Dana-Farber Cancer Institute, USA Kun-Mao Chao, National Taiwan University, Taiwan Jake Yue Chen, Indiana U. School of Informatics, USA Francis Chin, The University of Hong Kong, Hong Kong Jung Kyoon Choi, KAIST, Korea In-Sun Chu, KRIBB, Korea Kyungsook Han, INHA University, Korea Wen-Lian Hsu, Academia Sinica, Taiwan Jun Huan, U. of Kansas, USA Hsien-Da Huang, National Chiao Tung University, Taiwan Daniel Huson, University at Tubingen, Tubingen Jenn-Kang Hwang, National Chiao Tung University, Taiwan Ju Han Kim, Seoul National University, Korea Hyunju Lee, GIST, Korea Sang Yup Lee, KAIST, Korea Wentian Li, Feinstein Institute for Medical Research, USA Jingchu Luo, Peking University, China Bin Ma, University of Waterloo, Canada Hiroshi Mamitsuka, Kyoto University, Japan Geoff McLachlan, University of Queensland, Australia Satoru Miyano, University of Tokyo, Japan Shinichi Morishita, University of Tokyo, Japan Kenta Nakai, University of Tokyo, Japan Mark Ragan, University of Queensland, Australia Naren Ramakrishan, Graduate Studies (bio), India Cenk Sahinalp, SFU, Canada Yasubumi Sakakibara, Keio University, Japan David Sankoff, University of Ottawa, Canada Thomas Schlitt, King's College London, United Kingdon Narayanaswamy Srinivasan, IISc, India Alfonso Valencia, Centro Nacional de Biotechnologia, Spain Lusheng Wang, The City University of Hong Kong, Hong Kong Hong Yan, The City University of Hong Kong, Hong Kong Ueng Cheng Yang, National Yang Ming University, Taiwan S.M. Yiu, The University of Hong Kong, Hong Kong Kim Young, KRIBB, Korea Louxin Zhang, National University of Singapore, Singapore Xuegong Zhang, Tsinghua University, China Hongyu Zhao, Yale School of Public Health, USA From abualiga2 at gmail.com Thu Aug 25 10:51:35 2011 From: abualiga2 at gmail.com (galeb abu-ali) Date: Thu, 25 Aug 2011 10:51:35 -0400 Subject: [BiO BB] append schema to proxy In-Reply-To: References: Message-ID: Hi, I'm trying to run a program that generates a circular genome homology atlas "BLASTatlas" ( http://www.cbs.dtu.dk/ws/ws.php?entry=BLASTatlas ). I think the problem is with the module that appends schemas to the proxy, and I don't know how to do that manually. I've emailed the author couple times and have not heard back. Pasted below is the error message. At your convenience, I'd greatly appreciate your help. thanks galeb p/s - also, is there another program that can generate concetric circular plots of BLAST scores for multiple bacterial genomes with a per nucleotide resolution? thanks [galeb at localhost GeneWiz]$ BLASTatlas -modus circle -ref BX571966.fsa -proteins BX571966.proteins.fsa -ann BX571966.ann -blastcfg blast.cfg -customcfg custom.cfg --dnap="Intrinsic Curvature,Stacking Energy,Position Preference" -title "B. pseudomallei K96243" > sgeneric.ps # title set to 'B. pseudomallei K96243' # output format is ps # modus is 'circle' # loading reference genome ... # loading proteins ... # parsing blast lane configuration (blast.cfg) ... # .. parsing blast lane (B. ubonensis Bu) ... # .. .. program: tblastn # .. .. parsing color 101010_040410 # .. .. .. color from: r:10, g:10, b:10 # .. .. .. color to: r:04, g:04, b:10 # .. .. byrange: 0 .. 0.8 # .. parsing sequene source 'cat ./19539.fsa |' ... 1142 done # .. parsing blast lane (B. pseudomallei DM98) ... # .. .. program: tblastn # .. .. parsing color 101010_040410 # .. .. .. color from: r:10, g:10, b:10 # .. .. .. color to: r:04, g:04, b:10 # .. .. byrange: 0 .. 0.8 # .. parsing sequene source 'cat ./19509.fsa |' ... 2370 done # parsing custom lane configuration (custom.cfg) ... # .. parsing custom data entry SIDD at -0.035 ... # .. .. parsing color 000010_101010 # .. .. .. color from: r:00, g:00, b:10 # .. .. .. color to: r:10, g:10, b:10 # .. .. byrange: 9 .. 10 # .. .. boxfilter 5000 ... # .. parsing data source 'gunzip -c BX571966- 57a2f2c2e11ca0dd8cd74493d667d4d6-3173005.sidd--0.035-c-10-c.out.gz | cut -f4 |' ... # .. .. parsing data source ... 3173005 done # reading external files and build hash of sequences ... *panic: schemas() removed in v2.00, not needed anymore* at /usr/local/lib/perl5/site_perl/5.12.2/XML/Compile/WSDL11.pm line 65 XML::Compile::WSDL11::schemas(XML::Compile::WSDL11=HASH(0x1fed6740)) at xml-compile.pl line 48 main::appendSchemas(XML::Compile::WSDL11=HASH(0x1fed6740), " http://www.cbs.dtu.dk/ws/common/ws_common_1_0b.xsd", " http://www.cbs.dtu.dk/ws/BLASTatlas/ws_blastatlas_1_0_ws2.xsd") at BLASTatlas line 177appen From dan.bolser at gmail.com Thu Aug 25 18:04:43 2011 From: dan.bolser at gmail.com (Dan Bolser) Date: Thu, 25 Aug 2011 23:04:43 +0100 Subject: [BiO BB] append schema to proxy In-Reply-To: References: Message-ID: On 25 August 2011 15:51, galeb abu-ali wrote: > Hi, > > I'm trying to run a program that generates a circular genome homology atlas > "BLASTatlas" ( http://www.cbs.dtu.dk/ws/ws.php?entry=BLASTatlas ). I think > the problem is with the module that appends schemas to the proxy, and I > don't know how to do that manually. I've emailed the author couple times and > have not heard back. Pasted below is the error message. At your convenience, > I'd greatly appreciate your help. > > thanks > > galeb > > p/s - also, is there another program that can generate concetric circular > plots of BLAST scores for multiple bacterial genomes with a per nucleotide > resolution? thanks Since this looks like a Perl program, I've CC'ed this reply to the BioPerl mailing list in case anyone there can provide specific help. If I understood what you want to do, you could try Circos [1]. Why don't you keep the author of BLASTatlas CC'ed in these mails? Cheers, Dan. [1] http://circos.ca/ > [galeb at localhost GeneWiz]$ BLASTatlas -modus circle -ref BX571966.fsa > -proteins BX571966.proteins.fsa -ann BX571966.ann -blastcfg blast.cfg > -customcfg custom.cfg --dnap="Intrinsic Curvature,Stacking Energy,Position > Preference" -title "B. pseudomallei K96243" > ?sgeneric.ps > # title set to 'B. pseudomallei K96243' > # output format is ps > # modus is 'circle' > # loading reference genome ... > # loading proteins ... > # parsing blast lane configuration (blast.cfg) ... > # .. parsing blast lane (B. ubonensis Bu) ... > # .. .. program: tblastn > # .. .. parsing color 101010_040410 > # .. .. .. color from: r:10, g:10, b:10 > # .. .. .. color to: r:04, g:04, b:10 > # .. .. byrange: 0 .. 0.8 > # .. parsing sequene source 'cat ./19539.fsa |' ... 1142 done > # .. parsing blast lane (B. pseudomallei DM98) ... > # .. .. program: tblastn > # .. .. parsing color 101010_040410 > # .. .. .. color from: r:10, g:10, b:10 > # .. .. .. color to: r:04, g:04, b:10 > # .. .. byrange: 0 .. 0.8 > # .. parsing sequene source 'cat ./19509.fsa |' ... 2370 done > # parsing custom lane configuration (custom.cfg) ... > # .. parsing custom data entry SIDD at -0.035 ... > # .. .. parsing color 000010_101010 > # .. .. .. color from: r:00, g:00, b:10 > # .. .. .. color to: r:10, g:10, b:10 > # .. .. byrange: 9 .. 10 > # .. .. boxfilter 5000 ... > # .. parsing data source 'gunzip -c BX571966- > 57a2f2c2e11ca0dd8cd74493d667d4d6-3173005.sidd--0.035-c-10-c.out.gz | cut -f4 > |' ... > # .. .. parsing data source ... 3173005 done > # reading external files and build hash of sequences ... > *panic: schemas() removed in v2.00, not needed anymore* > ?at /usr/local/lib/perl5/site_perl/5.12.2/XML/Compile/WSDL11.pm line 65 > XML::Compile::WSDL11::schemas(XML::Compile::WSDL11=HASH(0x1fed6740)) at > xml-compile.pl line 48 > main::appendSchemas(XML::Compile::WSDL11=HASH(0x1fed6740), " > http://www.cbs.dtu.dk/ws/common/ws_common_1_0b.xsd", " > http://www.cbs.dtu.dk/ws/BLASTatlas/ws_blastatlas_1_0_ws2.xsd") at > BLASTatlas line 177appen > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > From thomas at cbs.dtu.dk Fri Aug 26 00:37:19 2011 From: thomas at cbs.dtu.dk (=?utf-8?B?VGhvbWFzIFNpY2hlcml0ei1Qb250ZW4g?=) Date: Fri, 26 Aug 2011 06:37:19 +0200 Subject: [BiO BB] =?utf-8?q?append_schema_to_proxy?= Message-ID: <20110826043721.F1A1D490@hermes.cbs.dtu.dk> I will print this message and tape it on the blastatlas groupleader's screen. Let me know if you haven't heard from them within a week, cheers /T -- Sicheritz-Ponten Thomas, Associate Professor, Ph.D Head of Metagenomics, Technical University of Denmark Center for Biological Sequence Analysis, BioCentrum CBS: +45 45 252422 ? ? ?Building 208, DK-2800 Lyngby Fax: +45 45 931585 ? ? ?http://www.cbs.dtu.dk/~thomas ----- Reply message ----- From: "Dan Bolser" Date: Fri, Aug 26, 2011 00:04 Subject: [BiO BB] append schema to proxy To: "General Forum at Bioinformatics.Org" On 25 August 2011 15:51, galeb abu-ali wrote: > Hi, > > I'm trying to run a program that generates a circular genome homology atlas > "BLASTatlas" ( http://www.cbs.dtu.dk/ws/ws.php?entry=BLASTatlas ). I think > the problem is with the module that appends schemas to the proxy, and I > don't know how to do that manually. I've emailed the author couple times and > have not heard back. Pasted below is the error message. At your convenience, > I'd greatly appreciate your help. > > thanks > > galeb > > p/s - also, is there another program that can generate concetric circular > plots of BLAST scores for multiple bacterial genomes with a per nucleotide > resolution? thanks Since this looks like a Perl program, I've CC'ed this reply to the BioPerl mailing list in case anyone there can provide specific help. If I understood what you want to do, you could try Circos [1]. Why don't you keep the author of BLASTatlas CC'ed in these mails? Cheers, Dan. [1] http://circos.ca/ > [galeb at localhost GeneWiz]$ BLASTatlas -modus circle -ref BX571966.fsa > -proteins BX571966.proteins.fsa -ann BX571966.ann -blastcfg blast.cfg > -customcfg custom.cfg --dnap="Intrinsic Curvature,Stacking Energy,Position > Preference" -title "B. pseudomallei K96243" > ?sgeneric.ps > # title set to 'B. pseudomallei K96243' > # output format is ps > # modus is 'circle' > # loading reference genome ... > # loading proteins ... > # parsing blast lane configuration (blast.cfg) ... > # .. parsing blast lane (B. ubonensis Bu) ... > # .. .. program: tblastn > # .. .. parsing color 101010_040410 > # .. .. .. color from: r:10, g:10, b:10 > # .. .. .. color to: r:04, g:04, b:10 > # .. .. byrange: 0 .. 0.8 > # .. parsing sequene source 'cat ./19539.fsa |' ... 1142 done > # .. parsing blast lane (B. pseudomallei DM98) ... > # .. .. program: tblastn > # .. .. parsing color 101010_040410 > # .. .. .. color from: r:10, g:10, b:10 > # .. .. .. color to: r:04, g:04, b:10 > # .. .. byrange: 0 .. 0.8 > # .. parsing sequene source 'cat ./19509.fsa |' ... 2370 done > # parsing custom lane configuration (custom.cfg) ... > # .. parsing custom data entry SIDD at -0.035 ... > # .. .. parsing color 000010_101010 > # .. .. .. color from: r:00, g:00, b:10 > # .. .. .. color to: r:10, g:10, b:10 > # .. .. byrange: 9 .. 10 > # .. .. boxfilter 5000 ... > # .. parsing data source 'gunzip -c BX571966- > 57a2f2c2e11ca0dd8cd74493d667d4d6-3173005.sidd--0.035-c-10-c.out.gz | cut -f4 > |' ... > # .. .. parsing data source ... 3173005 done > # reading external files and build hash of sequences ... > *panic: schemas() removed in v2.00, not needed anymore* > ?at /usr/local/lib/perl5/site_perl/5.12.2/XML/Compile/WSDL11.pm line 65 > XML::Compile::WSDL11::schemas(XML::Compile::WSDL11=HASH(0x1fed6740)) at > xml-compile.pl line 48 > main::appendSchemas(XML::Compile::WSDL11=HASH(0x1fed6740), " > http://www.cbs.dtu.dk/ws/common/ws_common_1_0b.xsd", " > http://www.cbs.dtu.dk/ws/BLASTatlas/ws_blastatlas_1_0_ws2.xsd") at > BLASTatlas line 177appen > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > _______________________________________________ BBB mailing list BBB at bioinformatics.org http://www.bioinformatics.org/mailman/listinfo/bbb