I have ~1700 EST sequences that I need to submit to genbank dbEST and for that It is necessary to fill a short form (.txt) for each one of the ESTs. I wonder if there is an easy tool to do that automatically.
Trace2dbest does exactly that - its part of the free PartiGene package (PUBMED ID: 14988115) - you'll need access to a linux machine, but there is good documentation and we have even had it running under OS X. Download from http://www.nematodes.org/bioinformatics/PartiGene/
Good luck!
John
Trace2dbest does exactly that - its part of the free PartiGene package (PUBMED ID: 14988115) - you'll need access to a linux machine, but there is good documentation and we have even had it running under OS X. Download from http://www.nematodes.org/bioinformatics/PartiGene/
Good luck!
John
You may want to also check out Taverna, an open source free tool for creating scientific workflows. The site has many existing scripts, plus there is an active user community. http://www.taverna.org.uk/
I used ESTin (http://pat.kobic.re.kr/estin/estin.html)
Described in:
Lee B: ESTin: a program for building a dbEST submission file from massive EST sequences. Genom Info 2006, 4:170-172.
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