Package: FASTA

FASTA - Pairwise and global similarity searches
Documentation
FASTA2 Package User's Guide	$doc/fasta/fasta20.txt
FASTA3 Package User's Guide	$doc/fasta/fasta3x.txt
File format specification	$doc/fasta/format.txt
Overall structure of fasta programs	$doc/fasta/fasta_func.txt
FASTA Web Site	http://www.people.virginia.edu/%7Ewrp/pearson.html
FASTA paper	http://people.virginia.edu/~wrp/papers/mmol98f.pdf
Data
Platforms: solaris-sparc, linux-intel, solaris-amd64, linux-x86_64
Installation: BIRCH
Programs:
align - Pairwise global sequence alignment bestscor - Calculate the score of a 100% identical match fasta - Sequence database similarity fastf - compare mixed peptides to a protein database fastm - compare ordered peptides (or short DNA sequences) to a protein or DNA database fasts - compare unordered peptides to a protein database fastx - Database similarity - allow frameshifts between codons fasty - Database similarity - Allow frameshifts within codons fromgb - garnier - Protein secondary structure ggsearch - global alignment of two DNA or protein sequences glsearch - global alignment of DNA or protein query sequence with local alignments of database sequences grease - Protein hydrophobicity lalign - Rigorous local pairwise alignment mrtrans - Align DNA sequences to a protein multiple alignment randseq - Randomize a set of sequences relate - Statistical significance of database similarity ssearch - Rigorous Smith-Waterman database similarity search tfasta - Database similarity with translated DNA database tfastf - compare mixed peptides to a translated DNA database tfasts - compare unordered peptides to a translated DNA database tfastx - compare a protein to a DNA database, calculating similarities with frameshifts tfasty - compare a protein to a DNA database, calculating similarities with frameshifts