fasta-36.3.8d

The FASTA package - protein and DNA sequence similarity searching and alignment programs

Changes in fasta-36.3.8d released 13-April-2016:

1. Various bug fixes to pssm_asn_subs.c that avoid coredumps when
   reading NCBI PSSM ASN.1 binary files. pssm_asn_subs.c can now read
   UUPACAA sequences.
2. default gap penalties for VT40 (from -14/-2 to -13/-1), VT80 (from
   -14/-2 to -11/-1), and VT120 (from -10/-1 to 11/-1) have changed
   slightly.
3. Introduction of scripts/m9B_btop_msa.pl and
   scripts/m8_btop_msa.pl, which uses the BTOP (-m 9B or -m 8CB)
   encoded alignment strings to produce a query driving multiple
   sequence alignment (MSA) in ClustalW format. This MSA can be used
   as input to psiblast to produce an ASN.1 PSSM.
4. The scripts/annot_blast_btop2.pl script replaces
   scripts/annot_blast_btop.pl and allows annotation of both the query
   and subject sequences.
5. Various domain annotation scripts have been renamed for clarity.
   For example, ann_feats_up_sql.pl uses an SQL implementation of
   Uniprot features tables to annotate domains. Likewise,
   ann_pfam_www.pl gets domain information from the Pfam web site,
   while ann_pfam27.pl gets the information from the downloaded
   Pfam27 mySQL tables, and ann_pfam28.pl uses the Pfam28 mySQL
   tables.
6. percent identity in sub-alignment scores is calculated like a BLAST
   percent identity -- gaps are not included in the denominator.

For more detailed information, see doc/readme.v36.