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Local FASTA search with multiple sequences

William R. Pearson wrp at alpha0.bioch.virginia.edu
Thu Mar 15 04:04:34 EST 2001

Rimantas.Plaipa at gf.vu.lt (Rimas) writes:

> MarkMcClain wrote:
> > 
> > I am interested in performing multiple FASTA searches on a local machine
> > (Mac or PC, possibly Linux) using a local database. When I submit a file
> > containing multiple sequences in FASTA format, (">string", sequence,
> > ">string2", sequence2...), the program does not recognize the beginning of a
> > new sequence and simply concatenates the two sequences to perform the
> > search. When I use the same file as input into BLAST, each sequence is
> > recognized as I intended.
> > 
> I have done this many times and it works. There may be problems if
> you're using foreign format files. For example, Unix text format
> libraries (with LF as line end char) doesn't work on PC.
> Maybe you are using Mac format file on PC or vice versa ?

If you can search with FASTA with multiple fasta query sequences, you are not
using the standard FASTA package on a Mac or PC.  None of the programs that
I distribute on those platforms work for multiple queries.

Under unix, you can search with several queries in a file using the
MPI or PVM parallel versions.  Unfortunately, the unix versions of the
standard fasta programs do not work with multiple queries.

Bill Pearson

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