Question

in-house blast DB creation

0

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10.2 years ago

tatsu1207 ▴ 10

Hello,

I hope this command line explains what I am asking...

makeblastdb -in a.fasta -dbtype prot
head -10 a.fasta >a.part.fasta
blastx -query a.part.fasta -db ./a.fasta

I got "No hits found" .... I thought I should not see any "no hits" since I am querying a fasta file to itself.

It seems to work fine when I made it nucleotide DB and executed blastn.

Please advise,

thanks for your help and time for my stupid question.

TU

blast • 2.1k views

ADD COMMENT • link updated 3.1 years ago by Ram 44k • written 10.2 years ago by tatsu1207 ▴ 10

Ram · Answer 1 · 2014-11-08

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10.2 years ago

rtliu ★ 2.2k

Use blastp for protein-protein BLAST.

ADD COMMENT • link updated 3.1 years ago by Ram 44k • written 10.2 years ago by rtliu ★ 2.2k

1

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Sorry , I should have mentioned.

a.fasta is a DNA sequence.

Thanks,
TU

ADD REPLY • link updated 3.1 years ago by Ram 44k • written 10.2 years ago by tatsu1207 ▴ 10

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makeblastdb -in a.fasta -dbtype nucl
blastn -query a.part.fasta -db a.fasta

ADD REPLY • link updated 3.1 years ago by Ram 44k • written 10.2 years ago by rtliu ★ 2.2k

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Yes, I tested it and it works fine with blastn.

I want blastx, so that users can query their DNA and know functions

Thanks,
TU

ADD REPLY • link updated 3.1 years ago by Ram 44k • written 10.2 years ago by tatsu1207 ▴ 10

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Hi rtliu,

Thanks for your reply, I just realized that all I have to do is tblastx.

Thanks for your time and sorry to have bothered!!!

TU

ADD REPLY • link updated 3.1 years ago by Ram 44k • written 10.2 years ago by tatsu1207 ▴ 10