FastA

Introduction

The FastA suite of programs provides methods for searching sequence databases and comparing sequences, as well as some more general analysis programs. FastA is based on a word, or tuple, search method which gives it its speed. Tuples are normally 4 to 6 for nucleic acids and 1 or 2 for amino acids. However, FastA cannot see matches of less than the tuple size. Generally, FastA is considered to be more sensitive than Blast, but somewhat slower. The most sensitive search uses the Smith-Waterman algorithm, but this is much slower. Psi-Blast, which iterates the database search using profiles, has also increased sensitivity.

FastA:

uses a local alignment method based on matching tuples.
has empirically determined match statistics, similar to Blast.
is more sensitive, but slower, if a smaller tuple size is used.
is best used by following some advice on sequence searching:
- from Steven Brenner.
- from Bill Pearson the author of FastA.

Programs and Documentation

FastA through the Web ( Documentation)
FastA at the EBI	FastA at Virginia	FastA at DDBJ
Smith-waterman searches at the EBI
ssearch3	fast, "true" S-W	blitz (Compugen)
GCG FastA Documentation
FastA	SSearch	TFastA
TFastX	FastX	FastA parsable output

Programs in the FastA suite (from the FastA documentation)

fasta3 Compare a protein sequence to a protein sequence database or a DNA sequence to a DNA sequence database using the FASTA algorithm. Search speed and selectivity are controlled with the ktup(word size) parameter. For protein comparisons, ktup = 2 by default; ktup =1 is more sensitive but slower. For DNA comparisons, ktup=6 by default; ktup=3 or ktup=4 provides higher sensitivity; ktup=1 should be used for oligonucleotides (DNA query lengths < 20).

fastx3
fasty3 Compare a DNA sequence to a protein sequence database, by comparing the translated DNA sequence in three frames and allowing gaps and frame shifts. fastx3 uses a simpler, faster algorithm for alignments that allows frame shifts only between codons; fasty3 is slower but produces better alignments with poor quality sequences because frame shifts are allowed within codons.

tfastx3
tfasty3 Compare a protein sequence to a DNA sequence database, calculating similarities with frame shifts to the forward and reverse orientations.

tfasta3 Compare a protein sequence to a DNA sequence database, calculating similarities (without frame shifts) to the 3 forward and three reverse reading frames. tfastx3 and tfasty3 are preferred because they calculate similarity over frame shifts.

ssearch3p Compare a protein sequence to a protein sequence database or a DNA sequence to a DNA sequence database using the Smith-Waterman algorithm. ssearch3 is about 10-times slower than FASTA3, but is more sensitive for full-length protein sequence comparison.

fastf3
tfastf3 Compares an ordered peptide mixture, as would be obtained by Edman degradation of a CNBr cleavage of a protein, against a protein (fastf) or DNA (tfastf) database.

fastf3
tfastf3 Compares set of short peptide fragments, as would be obtained from mass-spec. analysis of a protein, against a protein (fasts) or DNA (tfasts) database.

prss3 Evaluates the significance of pairwise similarity scores using a Monte Carlo analysis. Similarity scores for the two sequences are calculated, and then the second sequence is shuffled 200 to 1000 times and compared with the first sequence. prss3 can use one of two shuffling strategies. One strategy simply keeps the amino acid composition of the entire shuffled sequence identical to the unshuffled sequence. The second, local shuffle, destroys the order but preserves the composition of small (10 - 25 residue) segments of the shuffled sequence.

lfasta local similarity searches showing local alignments.

lalign A rigorous local sequence alignment program that will display the N-best local alignments. It incorporates the "sim" algorithm described by Huang and Miller (1991) Adv. Appl. Math. 12:337-357.

plalign A version of lalign that plots the local alignments to a postscript file.

flalign a version of lalign that plots the local alignments to a GCG Figure file.

prdf2 Calculates the probability of a similarity score more accurately by using a fit to an extreme value distribution.

align Optimal global alignment of two sequences

align0 As align, but does not penalize for end-gaps.

randseq Produces a randomly shuffled sequence from a query sequence.

crandseq Produces a randomly shuffled DNA sequence keeping the codons intact.

aacomp Calculates the amino acid composition and molecular weight of a sequence.

bestscor Calculates the best self-comparison score.

fromgb convert from GenBank LOCUS format to Pearson/FASTA format.

grease Kyte-Doolittle hydropathicity profile

tgrease Graphic plot of Kyte-Doolittle profile.

garnier A secondary structure prediction program using the method of Garnier, Osgusthorpe, and Robson, J. Mol. Biol., (1978) 120:97-120.

zs_exp takes a z-score (mean 50, s.d. 10) and converts it to an expectation value using the extreme value distribution and the size of the database

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Programs in the FastA suite (from the FastA documentation)
fasta3	Compare a protein sequence to a protein sequence database or a DNA sequence to a DNA sequence database using the FASTA algorithm. Search speed and selectivity are controlled with the ktup(word size) parameter. For protein comparisons, ktup = 2 by default; ktup =1 is more sensitive but slower. For DNA comparisons, ktup=6 by default; ktup=3 or ktup=4 provides higher sensitivity; ktup=1 should be used for oligonucleotides (DNA query lengths < 20).
fastx3 fasty3	Compare a DNA sequence to a protein sequence database, by comparing the translated DNA sequence in three frames and allowing gaps and frame shifts. fastx3 uses a simpler, faster algorithm for alignments that allows frame shifts only between codons; fasty3 is slower but produces better alignments with poor quality sequences because frame shifts are allowed within codons.
tfastx3 tfasty3	Compare a protein sequence to a DNA sequence database, calculating similarities with frame shifts to the forward and reverse orientations.
tfasta3	Compare a protein sequence to a DNA sequence database, calculating similarities (without frame shifts) to the 3 forward and three reverse reading frames. tfastx3 and tfasty3 are preferred because they calculate similarity over frame shifts.
ssearch3p	Compare a protein sequence to a protein sequence database or a DNA sequence to a DNA sequence database using the Smith-Waterman algorithm. ssearch3 is about 10-times slower than FASTA3, but is more sensitive for full-length protein sequence comparison.
fastf3 tfastf3	Compares an ordered peptide mixture, as would be obtained by Edman degradation of a CNBr cleavage of a protein, against a protein (fastf) or DNA (tfastf) database.
fastf3 tfastf3	Compares set of short peptide fragments, as would be obtained from mass-spec. analysis of a protein, against a protein (fasts) or DNA (tfasts) database.
prss3	Evaluates the significance of pairwise similarity scores using a Monte Carlo analysis. Similarity scores for the two sequences are calculated, and then the second sequence is shuffled 200 to 1000 times and compared with the first sequence. prss3 can use one of two shuffling strategies. One strategy simply keeps the amino acid composition of the entire shuffled sequence identical to the unshuffled sequence. The second, local shuffle, destroys the order but preserves the composition of small (10 - 25 residue) segments of the shuffled sequence.
lfasta	local similarity searches showing local alignments.
lalign	A rigorous local sequence alignment program that will display the N-best local alignments. It incorporates the "sim" algorithm described by Huang and Miller (1991) Adv. Appl. Math. 12:337-357.
plalign	A version of lalign that plots the local alignments to a postscript file.
flalign	a version of lalign that plots the local alignments to a GCG Figure file.
prdf2	Calculates the probability of a similarity score more accurately by using a fit to an extreme value distribution.
align	Optimal global alignment of two sequences
align0	As align, but does not penalize for end-gaps.
randseq	Produces a randomly shuffled sequence from a query sequence.
crandseq	Produces a randomly shuffled DNA sequence keeping the codons intact.
aacomp	Calculates the amino acid composition and molecular weight of a sequence.
bestscor	Calculates the best self-comparison score.
fromgb	convert from GenBank LOCUS format to Pearson/FASTA format.
grease	Kyte-Doolittle hydropathicity profile
tgrease	Graphic plot of Kyte-Doolittle profile.
garnier	A secondary structure prediction program using the method of Garnier, Osgusthorpe, and Robson, J. Mol. Biol., (1978) 120:97-120.
zs_exp	takes a z-score (mean 50, s.d. 10) and converts it to an expectation value using the extreme value distribution and the size of the database