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Old 09-21-2011, 06:28 AM   #1
psurana
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Default Finding a specific gene in transcriptome assembly

I have a few genes of interest which I want to check are present in my de novo transcriptome assembly. I was wondering if anyone knows a software or technique to do so.

Thanks in advance

Priyanka
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Old 09-21-2011, 07:04 AM   #2
dnusol
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I guess you could blast your genes of interest against the transcriptome or even grep a bit of the gene sequence in the transcriptome file

HTH

D.
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Old 09-21-2011, 07:20 AM   #3
psurana
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I guess I will try the grep method. Thank you.

Priyanka
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Old 09-21-2011, 10:13 PM   #4
tomc
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There is a perl "fastagrep" that might help if you have a fasta version of your transcriptome

http://nebc.nox.ac.uk/scripts/parse/fastagrep
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Old 09-22-2011, 01:14 PM   #5
psurana
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Thanks tomc
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