Fast statistical alignment
Encyclopedia
FSA is a multiple sequence alignment
program for aligning many proteins or RNAs or long genomic DNA sequences. Along with MUSCLE and MAFFT
, FSA is one of the few sequence alignment programs which can align datasets of hundreds or thousands of sequences. FSA uses a different optimization criterion which allows it to more reliably identify non-homologous sequences than these other programs, although this increased accuracy comes at the cost of decreased speed.
FSA is currently being used for projects including sequencing new worm genomes and analyzing in vivo transcription factor binding in flies.
and outputs alignments in FASTA format
or Stockholm format
.
Multiple sequence alignment
A multiple sequence alignment is a sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. In many cases, the input set of query sequences are assumed to have an evolutionary relationship by which they share a lineage and are descended from a common ancestor...
program for aligning many proteins or RNAs or long genomic DNA sequences. Along with MUSCLE and MAFFT
MAFFT
MAFFT is a multiple sequence alignment program for amino acid or nucleotide sequences. MAFFT is freely available for academic use, without any warranty.- External links :* * * at EBI* at GenomeNet* in MyHits, SIB...
, FSA is one of the few sequence alignment programs which can align datasets of hundreds or thousands of sequences. FSA uses a different optimization criterion which allows it to more reliably identify non-homologous sequences than these other programs, although this increased accuracy comes at the cost of decreased speed.
FSA is currently being used for projects including sequencing new worm genomes and analyzing in vivo transcription factor binding in flies.
Input/Output
This program accepts sequences in FASTA formatFASTA format
In bioinformatics, FASTA format is a text-based format for representing either nucleotide sequences or peptide sequences, in which nucleotides or amino acids are represented using single-letter codes. The format also allows for sequence names and comments to precede the sequences...
and outputs alignments in FASTA format
FASTA format
In bioinformatics, FASTA format is a text-based format for representing either nucleotide sequences or peptide sequences, in which nucleotides or amino acids are represented using single-letter codes. The format also allows for sequence names and comments to precede the sequences...
or Stockholm format
Stockholm format
Stockholm format is a Multiple sequence alignment format used by Pfam and Rfam to disseminate protein and RNA sequence alignments. The alignment editors...
.