[BiO BB] Blast comparison

stefan.grzybek at pharma.novartis.com stefan.grzybek at pharma.novartis.com
Fri Oct 3 02:43:14 EDT 2003

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,

                      "Liu Haifeng"                                                                                            
                      <lhaifeng at dso.org.sg>                   To:       <bio_bulletin_board at bioinformatics.org>                
                      Sent by:                                cc:                                                              
                      bio_bulletin_board-admin at bioinfo        Subject:  [BiO BB] Blast comparison                              
                                                              Category:       |-------------------------|                      
                                                                              | ( ) Action needed       |                      
                      03-10-2003 03:51                                        | ( ) Decision needed     |                      
                      Please respond to                                       | ( ) General Information |                      
                      bio_bulletin_board                                      |-------------------------|                      


I need to do comparisons between pairs of protein sequences.  I have
installed standalone Blast locally and would like to call it from my
program.  For using blastp, I am wondering if I can avoid to perform
formatdb first since I am comparing one sequence against another rather
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!


Haifeng Liu

BiO_Bulletin_Board maillist  -  BiO_Bulletin_Board at bioinformatics.org

More information about the BBB mailing list