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
