README
  By: Joseph Ryan <jfryan@bu.edu> 
Date: Thu Dec  1 14:45:30 EST 2005

The get_homeodomains_from_blast.pl script was described as a custom
Perl script that was used to extract homeodomain sequences from 
FASTA files in the manuscript 'The cnidarian-bilaterian ancestor
possessed at least 57 homeoboxes' (Ryan et. al, 2006).

This document describes the files in this directory.  These files
are needed to run this script.

SCRIPT:
get_homeodomains_from_blast.pl
    used to extract the homeodomains from the BLAST.

DATA FILES:
contigs_v_deuthbxs.blastx.tab
    tabbed output of BLASTX of Nematostella homeobox containing 
    contigs vs. a database of deuterostome homeodomains

contigs_v_deuthbxs.blastx
    same as contigs_v_deuthbxs.blastx.tab, but in BLAST report
    format.

frames.txt (contains the frames of the top hits from 
    frames of top hits culled from the "contigs_v_deuthbxs.blastx"
    file.

deut_homeobox_tis.fa.contigs
    Nematostella homeobox containing contigs

LIBRARIES:
NHGRI/FastaParser.pm
    Library developed at National Human Genome Research Institute
    used for parsing Fasta Files.

NHGRI/BioUtils.pm
    Library developed at National Human Genome Research Institute
    used for to translate nucleotides to proteins (nuc2prot)
    and reverse complement sequences (revcomp).

