FASTA sequence library on Mac?

Keith Robison robison at mito.harvard.edu
Mon Mar 20 18:04:46 EST 1995


Andy Law (Big Nose) (Andy.Law at bbsrc.ac.uk) wrote:
: I have the Mac version of FASTA downloaded and I want to run queries of
: locally generated sequences against other locally generated sequences.
: Currently I have to upload the sequences to our VAX, run the search, then
: reassemble the library incorporating the new sequences if appropriate
: using the GCG DATASET command.

: Has anyone written a utility for maintaining a local Mac sequence library
: compatible with the FASTA programs? I don't want to reinvent the wheel
: here.

FASTA format is trivial to maintain by hand, at least in my experience.
A sequence entry consists of name/comment line starting with '>',
followed by lines of sequence data.  I don't know about FASTA,
but BLAST is picky about all lines being the same length (except the
final line of a sequence).

i.e.:


>name  comments
aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
cccccccccccccccccccccccccccccccc
ttttttttttt


You should be able to just use your favorite text-editor, so long as
you save in Text-only  format.

Keith Robison
Harvard University
Department of Cellular and Developmental Biology
Department of Genetics / HHMI

robison at mito.harvard.edu 







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