FASTA moans and questions

Bill Pearson wrp at cyclops.micr.Virginia.EDU
Mon May 18 11:41:40 EST 1992

In article <9205181427.AA02797 at calshp.cals.wisc.edu> triplett at CALSHP.CALS.WISC.EDU writes:
>To Bill Pearson and GCG users:
>	I am also unable to use fasta to search through a specific 
>subset of sequences, specifically bacterial sequences.  Has GCG
>altered fasta such that this can no longer be done?  It is very 
>expensive to be searching through all of GenEMBL.
>Eric Triplett
>University of Wisconsin-Madison

	I was able to do this with the following commands to GCG:
(Note, GCG has modified FASTA, non-GCG users can search subsets of
the database by editing the FASTLIBS file.)

Bill Pearson

cyclops 40% fasta

FASTA does a Pearson and Lipman search for similarity between a
query sequence and any group of sequences.  FASTA answers the
question, "What sequences in the database are similar to my sequence?"
The relationship between FASTA and WORDSEARCH has not been
characterized, but FASTA is faster, and, for some searches, more

 FASTA with what query sequence ?  musgst.gb_ro

                  Begin (* 1 *) ?
                End (*  1018 *) ?

 Search for query in what sequence(s) (* GenEMBL:* *) ?  bacteria:*

 What word size (* 6 *) ?

 List how many best scores and alignments (* 40 *) ?

 What should I call the output file (* musgst.fasta *) ?

          1 Sequences       1,624 bp searched    GB_BA:ABCAARAA

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