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Big_blast and Standard blast

Keith James kdj at hgs2c.internal.sanger.ac.uk
Sun Feb 29 07:22:54 EST 2004

>>>>> " " == "Y Sun" <yudong.sun at ncl.ac.uk> writes:

   > Hi, Has anybody got the experience in comparing the outputs of
   > big_blast.pl and standard blast? Running on the same reference
   > and query sequences, I found that big_blast.pl reports much
   > more alignments than standard blast. Also, the extra alignments
   > are more than the consequence of cross-boundary matches. Does
   > anybody know the reason of such a phenomenom?


Is big_blast.pl a Perl script? It has the same name as a script used
internally by the PSU at the Sanger Institute, so I'm guessing that it
is has escaped into the wild.

PSU big_blast.pl is just a wrapper around either WU blast and/or NCBI
blast, so there may be no difference between the blast executable
being run by big_blast.pl and your "standard blast". I can't be sure
because you did not say which command line arguments you used in each
case. Be aware that big_blast.pl may well pass extra arguments to the
blast executable it runs.

Assuming that your script is from the PSU (it is the only hit on
Google) here are some things to check:

Are your "standard blast" and the blast executable being run by the
script the same?

Are the command line arguments passed to the executable the same in
each case?

It is very likely that one or both of these being different has caused
the result you are seeing.




- Keith James <kdj at sanger.ac.uk> Microarray Facility, Team 65 -
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK -

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