User: Scott Cain

gravatar for Scott Cain
Scott Cain750
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750
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Website:
http://gmod.org/
Last seen:
8 years, 3 months ago
Joined:
9 years, 5 months ago
Email:
1***@biostars.org

Posts by Scott Cain

<prev • 37 results • page 2 of 4 • next >
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Comment: C: Program To Visualize Gene Models With Highlighted Protein Features
... No, you don't need transparent glyphs, it would just make it really easy. You could also write your own glyph, which isn't real hard. ...
written 8.6 years ago by Scott Cain750
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Answer: A: Program To Visualize Gene Models With Highlighted Protein Features
... In an upcoming gbrowse release, we're getting ready to roll out new functionality that will allow transparent glyphs and I think you'd be able to do this, though it would be easier if you transform the protein coordinates to DNA coordinates. I don't have a release schedule, but we generally get the ...
written 8.6 years ago by Scott Cain750
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Answer: A: Gbrowse2 Mysql Indexing
... It is generally best to ask GBrowse questions on [the GBrowse mailing list](https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse), since there are many experienced users who follow the list. That said, Sean's suggestions make sense. When you say "hundreds of thousands of sequences" what do yo ...
written 8.7 years ago by Scott Cain750 • updated 10 months ago by RamRS28k
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Comment: C: Extracting Fasta Alignments From Parsed Blastxml File
... [BioPerl mailing list](http://lists.open-bio.org/mailman/listinfo/bioperl-l) ...
written 8.7 years ago by Scott Cain750 • updated 10 months ago by RamRS28k
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Answer: A: Which Bioperl Module Can I Use For Parsing/Mining Blast Output?
... And, should Michael's excellent suggestion not work out: http://lists.open-bio.org/mailman/listinfo/bioperl-l ...
written 8.7 years ago by Scott Cain750 • updated 10 months ago by RamRS28k
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Comment: C: Bioperl Seqio Reset (Next_Seq())
... Did you ask on [the bioperl mailing list](http://lists.open-bio.org/mailman/listinfo/bioperl-l)? It is a very active list. ...
written 8.7 years ago by Scott Cain750 • updated 10 months ago by RamRS28k
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Comment: C: Install Bioperl On Windows With Active Perl 5.14
... Did you ask on [the bioperl mailing list](http://lists.open-bio.org/mailman/listinfo/bioperl-l)? It is a very active list. ...
written 8.7 years ago by Scott Cain750 • updated 10 months ago by RamRS28k
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Comment: C: Gff Parsing In Biopython Is Not So Perfect
... Did you ask about this on the biopython mailing list? ...
written 8.8 years ago by Scott Cain750
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Answer: A: How To Convert Fasta To Gff?
... So the question is, what do you want to do with this data? I can think of one reason why you might want to create a GFF out of a fasta file: loading EST or cDNA sequences into a Chado database, for example, where you have to specify type and other attribute information during the load, and in fact ...
written 8.8 years ago by Scott Cain750
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Answer: A: Bacterial Annotation Pipeline
... The GMOD project has several alternatives, of which MAKER (mentioned above) is one, though it leans a little towards the euks. Another option which was designed for work with prokaryotes is DIYA (though looking at that page now it looks like SourceForge is messing with our wiki page). There is als ...
written 8.8 years ago by Scott Cain750

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