Package: FASTA
FASTA - Pairwise and global similarity searches
Documentation
File format specification
$doc/fasta/format.txt
User's Guide
$doc/fasta/fasta_guide.pdf
Manual
$doc/fasta/fasta36.1.html
User's Guide for FASTA2 programs
$doc/fasta/fasta20.pdf
Web site
https://github.com/wrpearson/fasta36
Data
Platforms
:
solaris-sparc, linux-intel, solaris-amd64, linux-x86_64, osx-x86_64
Installation
:
BIRCH
Programs
:
align - Pairwise global sequence alignment
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
map_db - read a FASTA (0), GENBANK flat file (1) PIR/VMS (5) or GCG binary (6) sequence database and produce the offsets necessary for efficient memory mapping
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
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