README

The BioTools are complete BioInformatics programs.

Database Searching and Alignment Tools:

  ProteinSearch - searches a list of protein FASTA databases with for protein sequences.
                - this program can identify evolutionarily related sequences deep into 
                  the twilight zone (as low as 5% sequence identity).

  AlignHits - generates protein multiple sequence alignments from ProteinSearch results
            - this program can align more than 20,000 protein sequences!


Parser Tools:

  GenBankParser - GenBank source file parser; generates FASTA files

  SwissProtParser - SwissProt source file parser; generates FASTA file


Utilities:

  lengths.pl - summarizes the lengths of sequences in a FASTA sequences file.

  Motifs.pl - identifies Prosite motifs in a protein FASTA sequences file.