me> On an unrelated topic, are there any plans by the people who
me> maintain the GenBank server to provide a means to restrict the amount of
me> output that BLAST returns?
DaveK> We have implemented a mail split program which will cut messages down
DaveK> to 100kb each and send them in series. This should be installed on the
DaveK> server soon. We have not had time yet to investigate alternate ways
DaveK> of cutting off BLAST input, but may implement something along the
DaveK> lines of our FASTA server to specify the number of alignments in the
DaveK> output (we want to avoid having to modify the original program if at
DaveK> all possible). We may also need to collect some stats on how large
DaveK> the typical output file is before proceeding with this.
Although it would take more work, being able to specify the number
of alignments to be returned would be the preferable approach by far from
the user's point of view. It would be a waste of time, not to mention a
waste of network bandwidth, to send and then read through or (gasp) print a
thousand alignments if your query sequence happens to be frequently
represented in the database. A couple of dozen good matches is sufficient to
determine what your sequence is related to. On the other hand, it could be
really useful to have the option of getting the output sorted in the reverse
order, ie, with the least related sequences first, for those times when you
want to identify the most distantly related sequences in a gene family.
Obviously a cut-off value would be necessary if this option is ever
implemented.
Just a suggestion.
Stephen Clark
clark at galen.oci.utoronto.ca (Internet)
clark at utoroci (Netnorth/Bitnet)
"For what it is worth, many of the legends accompanying figures in this journal
are not very different, although we take some care to provide each sentence
with a verb if the author has overlooked the need for one." -J.Maddox, Nature.
