Bioperl: RE: BioPerl for transcriptional profiling

Mark Evans Mark Evans" <
14 Sep 99 13:51:21 -0700

You might consider taking a look at the EST Exctracter BLAST program at  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

On 9/14/99, Chris Dagdigian wrote:
>Dr. Ebbole --
>I'm CC'ing this reply to the general bioperl >discussion list
>as there may be people there who have done similar >work
>or may even be at your University and will be better >positioned
>with advice...
>The best (short) answer I have for you is that yes >the BioPerl
>codebase may be helpful to your project but it is not >in a form
>that would be useful right out of the 'box' to a non-
>perl user
>or programmer. Generally speaking our software has >been used
>most successfully by sites that have programmers who >are able to
>take bioperl code and modules and integrate it into >systems they are
>building themselves. >
>What you are trying to do seems fairly >straightforward -- aligning some
>ESTs to create contigs and then BLASTing them >repeatedly looking
>for new homologies. There may be commercial or free >software out
>there that can already do all (or 90%) of these >things for you without needing >a resident stable of bioinformaticians or >programmers...perhaps others
>on this list can make additional suggestions.
>Chris >
>>>> "Dr. Daniel Ebbole" <> 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
>Dan >-- >Daniel Ebbole
>Associate Professor >Program for the Biology of Filamentous Fungi >Dept of Plant Pathology and Microbiology >Texas A&M University
>College Station, TX 77843-2132
>USA >Ph.409-845-4831 >Fax.409-845-6483
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