FASTA moans and questions

Fri May 15 12:11:00 EST 1992

Dear colleagues,
  I frequently use FASTA in my work. The latest version has some useful
improvements, eg. the whole sequence entry is not listed in alignments
when only a short match is found. However, I'd like to have a bit of a
moan and to ask some questions...

1. You used to be able to search sub-sets of the database, eg. B=
   Bacterial sequences. I found this most useful.

2. What is the meaning of the message "ignoring..(list of entry codes)"?

3. The best matches are listed as entry codes only. You used to get a
   short descriptor. "M21579" does not tell you much!

4. Is there a problem with the numbering of long sequences in alignments
   ?? eg MIPACGA (Embl) is over 100kb. The numbering goes from 99990 to
   10000 ! Whilst pretty obvious at present, this might prove to be an
   important fault as longer sequences or melded entries accumulate.

5. In local comparisons (LFasta) why should the order of comparison 
   sometimes give different answers? ie. it is not intuitive why 
   a compared to b should not be the same as b to a...

Sorry if this sounds a bit negative-in fact I find it a very useful
and powerful tool but I would like to see the points above addressed.

Best wishes,
Jim Brannigan

Chemistry Dept.
University of York, UK.

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