[BiO BB] Blast comparison

[stefan.grzybek at pharma.novartis.com]

Dear Haifeng,

you might want to use bl2seq. It is part of the NCBI blast distribution and
allows you to compare just two sequences by any one of the blast algorithms
(blast[npx], tblast[nx]).

Best regards,
Stefan



                                                                                                                               
                      "Liu Haifeng"                                                                                            
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Hi,

I need to do comparisons between pairs of protein sequences.  I have
installed standalone Blast locally and would like to call it from my
bioperl
program.  For using blastp, I am wondering if I can avoid to perform
formatdb first since I am comparing one sequence against another rather
than
searching one sequence against a set of sequences?  I guess it must be
stupid to format a single sequence into a blast DB whenever I want to
perform a comparison.  I will appreciate your any advices and help on the
matter.  Thank you!

Sincerely

Haifeng Liu

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