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fasta-v36.3.8g
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@wrpearson wrpearson released this 31 Dec 21:51
· 249 commits to v36.3.8 since this release
fasta-v36.3.8g
a7ae61f

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

Changes in fasta-36.3.8g released October, 2018

  1. psisearch2/m89_btop_msa2.pl

    1. the --clustal option produces a "CLUSTALW (1.8)", which is required for some downstream programs

    2. the --trunc_acc option removes the database and accession from identifiers of the form:
      sp|P09488|GSTM1_HUMAN to produce GSTM1_HUMAN.

    3. the --min_align option specifies the fraction of the query sequence that must be aligned
      (q_end-q_start+1)/q_length)

    Together, these changes make it possible for the output of m89_btop_msa2.pl to be used by
    the EMBOSS program fprotdist.

  2. A more general implementation of psisearch2_msa_iter.sh, which does psisearch2 one iteration at a time, and a new equivalent psisearch2_msa_iter_bl.sh, which uses psiblast to do the search.

  3. A small restructuring of the make/Makefiles to remove the -lz dependence for non-debugging scripts (and add it back when -DDEBUG is used).

Changes in fasta-36.3.8g released 5-Aug-2018

  1. (Apr 2018) incorporation of "-t t" temrination codes ("*") in -m 8CB, -m 8CC, and -m9C so that aligned termination codons are indicated as "**" (-m8CB) or
    "*1" (-m8CC, -m9C).

  2. (Mar 2018) Updates to scripts/annot_blast_btop2.pl to provide
    subalignment scoring for blastp searches (BLOSUM62 only). (see
    doc/readme.v36)

  3. (Feb. 2018) a new extended option, -XB, which causes percent
    identity, percent similarity, and alignment length to be calculated
    using the BLAST model, which does not count gaps in the alignment
    length.

see readme.v36 for other bug fixes.

Changes in fasta-36.3.8g released 31-Dec-2017

  1. (December, 2017) -- Make statistical thresholds more robust for
    small E()-values with normally distributed scores (ggsearch36,
    glsearch36).

  2. (September, 2017) Treat all lower-case queries as uppercase with -S option.

  3. (May, 2017) Improvements/fixes to sub-alignment scoring strategies.

  4. Improvements/fixes to psisearch2 scripts.

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

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