Bioperl: RE: BioPerl for transcriptional profiling

[Alessandro Guffanti]

Hi. Thanks for the citation.
The updated link to the EST Extractor is now

http://hercules.tigem.it/BLASTEXTRACT/estextract.html

but the one cited still works, buit may have problems with DNS
sometimes.

May I also suggest to give a look in general at
http://www.tigem.it/LOCAL/sequtils.html, in particular
the CAP Assembler (interactive assembly of FastA sequences) & CompBlast
(DIY Blast service) should be fit to Dr. Ebbole's problem.
The Cap2 / Cap3 assembly programs are (were ?) public domain 
programs from X.Huang: huang@paracel.com. The graphical
interface for NCBI Blast parsing is also public domain:
http://hercules.tigem.it/Biomodules.html.

Best Wishes,

Alessandro.

Mark Evans wrote:
> 
> You might consider taking a look at the EST Exctracter BLAST program at http://gcg.tigem.it/BLASTEXTRACT/estextract.html.  It does iterative BLAST and will generate a consensus derived from the hits.
> Mark Evans
> Bioinformatics Programmer/Analyst
> Invitrogen Corp
> 1600 Faraday Ave.
> Carlsbad, CA 92008
> evansm@invitrogen.com
> 800.955.6288x218

> >>>> "Dr. Daniel Ebbole" <d-ebbole@tamu.edu> 09/11 >11:47 AM >>>
> >Hello, I was browsing through the list of >participants of BioPerl and
> >found your interest in high throughput cDNA sequence >analysis. I know
> >nothing about the specifics of Perl. We are a little >shorthanded on
> >bioinformatics people here at the moment.  I work >with Neurospora crassa
> >and about 10,000 cDNA sequences are available in >GenBank.  The
> >sequencers who put the data there have limited >resources/ability to
> >analyze this data sufficiently.  I would like to >organize the data to
> >facilitate transcriptional profiling efforts.  The >things I would like
> >to do is sort all the ESTs into their overlapping >sets (defining a
> >minimal set of EST sequences for profiling) and make >contigs to create
> >files for frequent BLASTing for homology searches for >unknown genes.  Is
> >Perl/BioPerl something I should be looking into to >help me accomplish
> >this?
> >Dan >-- >Daniel Ebbole
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