AMAP
Encyclopedia
AMAP is a multiple sequence alignment
program based on a new approach to multiple alignment called sequence annealing. This approach consists of building up the multiple alignment one match at a time, thereby circumventing many of the problems of progressive alignment. The AMAP parameters can be used to tune the sensivitiy-specificity tradeoff.
The program can be used through the AMAP web server or as a standalone program which can be installed with the source code.
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The output format includes: FASTA format
, Clustal
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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 based on a new approach to multiple alignment called sequence annealing. This approach consists of building up the multiple alignment one match at a time, thereby circumventing many of the problems of progressive alignment. The AMAP parameters can be used to tune the sensivitiy-specificity tradeoff.
The program can be used through the AMAP web server or as a standalone program which can be installed with the source code.
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...
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The output format includes: 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...
, Clustal
Clustal
Clustal is a widely used multiple sequence alignment computer program. The latest version is 2.1. There are two main variations:*ClustalW: command line interface*ClustalX: This version has a graphical user interface...
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