Blat Hg19 Protein Search

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Entering edit mode

11.2 years ago

parker.dewaal • 0

Hello Biostarers,

I'm currently trying to use blat to search the hg19 database for small AA sequences (10-12 AA in length) however I'm having a difficult time getting actual output from my gfClient commands and the resulting files always appear to be blank. I believe my setup is correct, as in using the -trans flag for the gfServer and -q=prot -t=dnax for gfClient flags however I may be incorrect.

Here are the commands I've run to start the gfServer and gfClient:

gfServer -trans -mask start localhost 8127 hg19.2bit &

gfClient localhost 8127 /home/pdewaal/hg19/hg19.2bit test.fa output.psl -q=prot -t=dnax

additionally here is my test.fa file

LLVYVTQAAV

If anyone could provide some insight I would be greatly appreciative.

Cheers

blat hg19 protein • 2.5k views

ADD COMMENT • link 11.2 years ago by parker.dewaal • 0

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Entering edit mode

My guess is maybe your query is too short for the default BLAT parameters. eg. minScore

ADD REPLY • link 11.2 years ago by Torst ▴ 980

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