hi

i am working on a paper nameing DNA computing...
can any one of u help me if have any information regarding this

thanking you

alok kumar
pune (INDIA)

On Wed, 10 Sep 2003 bio_bulletin_board-request@bioinformatics.org 
wrote :
>When replying, PLEASE edit your Subject line so it is more 
>specific
>than "Re: BiO_Bulletin_Board digest, Vol..."
>
>
>Today's Topics:
>
>    1. BLASTing SCO (re: Linux IP, IBM suite, shred algorithm, 
>etc) (Harry Mangalam)
>    2. NCBI Viewer (jinal jhaveri)
>    3. Poly A tail length - script help please (Tristan 
>Fiedler)
>    4. Re: Poly A tail length - script help please (Joseph 
>Landman)
>    5. Re: Poly A tail length - script help please (Dmitri I 
>GOULIAEV)
>
>--__--__--
>
>Message: 1
>Date: Tue, 09 Sep 2003 09:13:26 -0700
> From: Harry Mangalam <hjm@tacgi.com>
>To: bio_bulletin_board@bioinformatics.org
>Subject: [BiO BB] BLASTing SCO (re: Linux IP, IBM suite, shred 
>algorithm, etc)
>Reply-To: bio_bulletin_board@bioinformatics.org
>
>I've been watching the SCO vs IBM suit with some interest and 
>this piqued my
>interest.
>
>Eric Raymond has apparently reworked some old 'shred' code which 
>calculates MD5
>hashes for long (from the molbio perspective) words (~3 lines at 
>a time) and
>then sorts the hashes to identify sections of the Linux source 
>code tree  which
>are identical to those from SCO-owned System V Unix base.
>
>This sounds a bit like the initial pass for BLAT, which generates 
>hashes for
>much smaller words and uses the hashes in comparisons.
>
>http://www.eweek.com/article2/0,4149,1257617,00.asp
>
>Could BLAST not be used to faster & much more sensitively 
>identify not only
>identical but similar sections of code?
>
>It would have to be modified to do an 'all against all' approach 
>and would have
>to  also take into account line numbers and file names, but 
>here'a a good
>undergrad programming project for someone, with the possibility 
>of getting some
>good press and creating a tool that will undoubtedly be used 
>again in litigation
>(read: it could be worth real money)
>
>Then again, the Raymond's shred code approach is probably good 
>enough.
>
>Comments?
>--
>Cheers, Harry
>Harry J Mangalam - 949 856 2847 (v&f) - hjm@tacgi.com
>              <<plain text preferred>>
>
>
>--__--__--
>
>Message: 2
>Date: Tue, 09 Sep 2003 12:03:45 -0700
> From: jinal jhaveri <jhaveri@usc.edu>
>To: bio_bulletin_board@bioinformatics.org
>Subject: [BiO BB] NCBI Viewer
>Reply-To: bio_bulletin_board@bioinformatics.org
>
>Hi there,
>
>I am developing a zoom viewer for chromosomes. Can any one give 
>tips on
>some available software to use for that. I want this zoom viewer 
>to be
>online (same as the one ncbi has
>(http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?org=arabid&chr=I) , 
>i.e
>the entrez one.
>
>thank you
>--Jinal
>
>
>--__--__--
>
>Message: 3
>Date: Tue, 9 Sep 2003 17:00:55 -0400 (EDT)
> From: "Tristan Fiedler" <tfiedler@rsmas.miami.edu>
>To: bio_bulletin_board@bioinformatics.org
>Cc: bio_bulletin_board@bioinformatics.org
>Subject: [BiO BB] Poly A tail length - script help please
>Reply-To: bio_bulletin_board@bioinformatics.org
>
>Thanks for the scripting tips!  I have a 'counting' issue which I 
>need to
>quickly resolve.  A typical sequence input file (5 - 700 bases) 
>looks like
>:
>
>AGTAGTCGATCATNATANCTANTACNACTACTAACTATGCTAGNNAATATAAAAAAAAANAAA
>
>I have over 500 files, named *.seq.  I would like to create a 
>script which :
>
>a.  runs through all the files,
>b.  counts the length of the 'poly A' tail (defined as the 
>longest stretch
>of A or N)
>c. sends the output to a file, eg.
>
>25 1.seq
>87 2.seq
>13 3.seq
>
>Example valid poly A tails :
>
>AAAANANANANAAANNAAAAAA
>
>AAAAAAAAAAAAAA
>
>NNNNNNNNNNNNN
>
>AAANNNNNNNNNNNAAAAAAAAA
>
>Thank you so much for your expertise!
>
>Tristan
>
>--
>Tristan J. Fiedler, Ph.D.
>Postdoctoral Research Fellow
>NIEHS Marine & Freshwater Biomedical Sciences Center
>Rosenstiel School of Marine & Atmospheric Sciences
>University of Miami
>
>tfiedler@rsmas.miami.edu
>t.fiedler@umiami.edu (alias)
>305-361-4626
>
>--__--__--
>
>Message: 4
>Subject: Re: [BiO BB] Poly A tail length - script help please
> From: Joseph Landman <landman@scalableinformatics.com>
>To: BiO BB <bio_bulletin_board@bioinformatics.org>
>Cc: biodevelopers <biodevelopers@bioinformatics.org>
>Date: Tue, 09 Sep 2003 19:57:34 -0400
>Reply-To: bio_bulletin_board@bioinformatics.org
>
>First one is free ...
>
>         #!/usr/bin/perl
>
>         use strict;
>
>         my 
>($directory,$directory_handle,$file,@files,$sequence);
>         my ($file_handle,$poly_a_tail,$rseq);
>
>         $directory = "./";	# directory to open
>         if (!(opendir $directory_handle,$directory))
>            {
>              die "FATAL ERROR: Unable to open directory = 
>".$directory."\n";
>            }
>
>         # select only the .seq files
>         @files = grep { /\.seq$/ } readdir($directory_handle);
>
>         # loop over these selected files
>         foreach $file (@files)
>           {
>             # try to open the file
>             if (!(open($file_handle,"< ".$file)))
>                {
>                  # if we cannot open it, warn the user, and skip 
>to the next file
>                  warn "Warning: unable to open file = 
>".$file."\. Skipping\.\n";
>         	 next;
>                }
>               else
>                {
>                  # assume one line per file, or we will have to 
>modify this
>         	 chomp($sequence=<$file_handle>);
>         	 # now time to bring out the heavy artillery
>         	 $rseq=reverse $sequence;	# poly-a is now at the head
>         	 $rseq =~ /^([AN]+)\w+$/;	# match A's and/or N's at the 
>front
>         	 $poly_a_tail = $1;		# return the match ...
>         	 printf "%i %s\n",length($poly_a_tail),$file;	# tell 
>the world ...
>         	 close($file_handle);
>                }
>           }
>
>
>
>On Tue, 2003-09-09 at 17:00, Tristan Fiedler wrote:
> > Thanks for the scripting tips!  I have a 'counting' issue 
>which I need to
> > quickly resolve.  A typical sequence input file (5 - 700 
>bases) looks like
> > :
> >
> > 
>AGTAGTCGATCATNATANCTANTACNACTACTAACTATGCTAGNNAATATAAAAAAAAANAAA
> >
> > I have over 500 files, named *.seq.  I would like to create a 
>script which :
> >
> > a.  runs through all the files,
> > b.  counts the length of the 'poly A' tail (defined as the 
>longest stretch
> > of A or N)
> > c. sends the output to a file, eg.
> >
> > 25 1.seq
> > 87 2.seq
> > 13 3.seq
> >
> > Example valid poly A tails :
> >
> > AAAANANANANAAANNAAAAAA
> >
> > AAAAAAAAAAAAAA
> >
> > NNNNNNNNNNNNN
> >
> > AAANNNNNNNNNNNAAAAAAAAA
> >
> > Thank you so much for your expertise!
> >
> > Tristan
>--
>Joseph Landman, Ph.D
>Scalable Informatics LLC
>email: landman@scalableinformatics.com
>   web: http://scalableinformatics.com
>phone: +1 734 612 4615
>
>
>
>--__--__--
>
>Message: 5
>Date: Wed, 10 Sep 2003 10:43:42 -0500
> From: Dmitri I GOULIAEV <dig@bioinformatics.org>
>To: bio_bulletin_board@bioinformatics.org
>Subject: Re: [BiO BB] Poly A tail length - script help please
>Organization: DIG
>Reply-To: bio_bulletin_board@bioinformatics.org
>
>Hi, Tristan Fiedler !
>
>  On Tue, Sep 09, 2003 at 05:00:55PM -0400, Tristan Fiedler 
>wrote:
>
> > Thanks for the scripting tips!  I have a 'counting' issue 
>which I need to
> > quickly resolve.  A typical sequence input file (5 - 700 
>bases) looks like
> > :
> >
> > 
>AGTAGTCGATCATNATANCTANTACNACTACTAACTATGCTAGNNAATATAAAAAAAAANAAA
> >
> > I have over 500 files, named *.seq.  I would like to create a 
>script which :
> >
> > a.  runs through all the files,
> > b.  counts the length of the 'poly A' tail (defined as the 
>longest stretch
> > of A or N)
> > c. sends the output to a file, eg.
> >
> > 25 1.seq
> > 87 2.seq
> > 13 3.seq
> >
> > Example valid poly A tails :
> >
> > AAAANANANANAAANNAAAAAA
> >
> > AAAAAAAAAAAAAA
> >
> > NNNNNNNNNNNNN
> >
> > AAANNNNNNNNNNNAAAAAAAAA
>
>If you have this sequences:
>
>     1.seq CACATGACTGACTGACTGACTACGACTGCAAAANANANANAAANNAAAAAA
>     2.seq CGTAGCTCTACGATGCTACGAGAAAAAAAAAAAAAA
>     3.seq TGTACGTACGATCGATGCTAGCNNNNNNNNNNNN
>     4.seq CATGTGCTACGACGATGCT
>     5.seq CATGTGCTACGACGATGCTAAAANNNNNNNNNNNAAAAAAAAA
>
>and you run this command:
>
>     $ for s in *.seq ; do cat $s | grep -o '[AN]*[AN]$' \
> 	| tr -d '\n' | wc -c | tr -d '\n' ; echo -e "\t$s" ; done
>
>then the output will be:
>
>      22 1.seq
>      14 2.seq
>      12 3.seq
>       0 4.seq
>      24 5.seq
>
>Exercise for the OP: redirect this output to a file.
>
> > Thank you so much for your expertise!
>
>You should really start learning the un*x text utilities and/or 
>some scripting language (e.g. python, tcl, perl).
>
>
>Regards,
>
>--
>DIG (Dmitri I GOULIAEV)        
>http://www.bioinformatics.org/~dig/
>1024D/63A6C649: 26A0 E4D5 AB3F C2D4 0112  66CD 4343 C0AF 63A6 
>C649
>
>
>--__--__--
>
>_______________________________________________
>BiO_Bulletin_Board maillist  -  
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>
>End of BiO_Bulletin_Board Digest

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