AMAP is a
multiple sequence alignment
Multiple sequence alignment (MSA) may refer to the process or the result of 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 evolutio ...
program based on
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 format
In bioinformatics and biochemistry, the FASTA format is a text-based format for representing either nucleotide sequences or amino acid (protein) sequences, in which nucleotides or amino acids are represented using single-letter codes. The format a ...
.
The output format includes:
FASTA format
In bioinformatics and biochemistry, the FASTA format is a text-based format for representing either nucleotide sequences or amino acid (protein) sequences, in which nucleotides or amino acids are represented using single-letter codes. The format a ...
,
Clustal
Clustal is a series of widely used computer programs used in bioinformatics for multiple sequence alignment. There have been many versions of Clustal over the development of the algorithm that are listed below. The analysis of each tool and its a ...
.
References
{{reflist
External links
AMAP web server
Bioinformatics software