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EMBOSS is an acronym for European Molecular Biology Open Software Suite. The European part of the name hints at the wider scope. The core EMBOSS groups are collaborating with many other groups to develop the new applications that the users need. This was done from the beginning with EMBnet, the European Molecular Biology Network. EMBnet has ...
Alignment of 27 avian influenza hemagglutinin protein sequences colored by residue conservation (top) and residue properties (bottom) Multiple sequence alignment is an extension of pairwise alignment to incorporate more than two sequences at a time. Multiple alignment methods try to align all of the sequences in a given query set.
T-Coffee calculates pairwise alignments by combining the direct alignment of the pair with indirect alignments that aligns each sequence of the pair to a third sequence. It uses the output from Clustal as well as another local alignment program LALIGN, which finds multiple regions of local alignment between two sequences.
SPA: Super pairwise alignment Fast pairwise global alignment: Nucleotide: Global: Shen, Yang, Yao, Hwang: 2002 SSEARCH Local (Smith-Waterman) alignment with statistics: Protein: Local: W. Pearson: 1981 (Algorithm) Sequences Studio Java applet demonstrating various algorithms from [27] Generic sequence: Local and global: A.Meskauskas: 1997 ...
This page is a subsection of the list of sequence alignment software. Multiple alignment visualization tools typically serve four purposes: Aid general understanding of large-scale DNA or protein alignments; Visualize alignments for figures and publication; Manually edit and curate automatically generated alignments; Analysis in depth
This list of structural comparison and alignment software is a compilation of software tools and web portals used in pairwise or multiple structural comparison and structural alignment. Structural comparison and alignment
Popular tools for sequence alignment include: Pair-wise alignment - BLAST, Dot plots; Multiple alignment - ClustalW, PROBCONS, MUSCLE, MAFFT, and T-Coffee. A common use for pairwise sequence alignment is to take a sequence of interest and compare it to all known sequences in a database to identify homologous sequences. In general, the matches ...
Skipredudant EMBOSS tool [19] to remove redundant sequences from a set; CLUSS Algorithm [20] to identify groups of structurally, functionally, or evolutionarily related hard-to-align protein sequences. CLUSS webserver [21] CLUSS2 Algorithm [22] for clustering families of hard-to-align protein sequences with multiple biological functions.