>> 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 ?