In bioinformatics, a sequence alignment is a way of arranging the primary sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences.
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multiple sequence alignment (MSA) is a sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. In general, the input set of query sequences are assumed to have an evolutionary relationship by which they share a lineage and are descended from a
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This list of structural alignment software is a compilation of software tools and web portals used in pairwise or multiple structural alignment

Structural alignment

NAME Description Class Type Link Author Year
MAMMOTH MAtching Molecular Models
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Structural alignment is a form of sequence alignment based on comparison of shape. These alignments attempt to establish equivalences between two or more polymer structures based on their shape and three-dimensional conformation.
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FASTA is a DNA and Protein sequence alignment software package first described (as FASTP) by David J. Lipman and William R. Pearson in 1985 in the article Rapid and sensitive protein similarity searches .
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A blast is an explosion. Blast can also refer to:

Entertainment:

• BBC Blast, a programme, website and tour for 13 - 19 year olds getting creative
• Blast (venue), an Irish concert organiser for alternative music groups
• Blast!

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JAligner is an open source Java implementation of the Smith-Waterman algorithm^[1] with Gotoh's improvement^[2] for biological local pairwise sequence alignment using the affine gap penalty model. Is was written by Ahmed Moustafa.
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Clustal is a widely used multiple sequence alignment computer program. The latest version is 1.83. There are two main variations:

• ClustalW: command line interface
• ClustalX: This version has a graphical user interface.

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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.
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ProbCons is an open source probabilistic consistency-based multiple alignment of amino acid sequences. It is an efficient protein multiple sequence alignment program, which has demonstrated a statistically significant improvement in accuracy compared to several leading alignment
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MAVID is a multiple sequence alignment program suitable for the alignment of large numbers of DNA sequences. The sequences can be small mitochondrial genomes or large genomic regions up to megabases long. The latest version is 2.0.4.
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MUSCLE (multiple sequence comparison by log-expectation) is public domain, multiple sequence alignment software for protein and nucleotide sequences.
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MAFFT is a multiple sequence alignment program for amino acid or nucleotide sequences.

MAFFT is freely available for academic use, without any warranty.

See also

• Sequence alignment software
• Clustal

References

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T-Coffee (Tree-based Consistency Objective Function For alignment Evaluation) is a multiple sequence alignment software using a progressive approach. It generates a library of pairwise alignments to guide the multiple sequence alignment.
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Sequerome is a web-based Sequence profiling tool developed by the Bioinformatics and Computational Biosciences Unit ( BCBU ) at Georgetown University. This tool, which is the only one of its kind, provides the unique and useful functionality of seamlessly integrating an entire
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Sim4 is a nucleotide sequence alignment program akin to BLAST but specifically tailored to DNA to cDNA/EST (Expressed Sequence Tag) alignment (as opposed to DNA-DNA or protein-protein alignment). It was written by Florea et al.
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PubMed Central is a free digital database of full-text scientific literature in biomedical and life sciences. It can be reached at [1] .

It grew from the online Entrez PubMed biomedical literature search system. PubMed Central was developed by the U.S.
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