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in-house blast DB creation

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
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updated by Ram Ram • written by tatsu1207 • tatsu1207

1 answer

Use blastp for protein-protein BLAST.

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updated by Ram Ram • written by rtliu rtliu

Sorry , I should have mentioned.

a.fasta is a DNA sequence.

Thanks,
TU

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updated by Ram Ram • written by tatsu1207 • tatsu1207

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

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updated by Ram Ram • written by tatsu1207 • tatsu1207

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

• 0 views • link
updated by Ram Ram • written by tatsu1207 • tatsu1207

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