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This list of sequence alignment software is a compilation of software tools and web portals used in pairwise sequence alignment and multiple sequence alignment. See structural alignment software for structural alignment of proteins.
In bioinformatics, a sequence alignment is a way of arranging the 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. [1] Aligned sequences of nucleotide or amino acid residues are typically represented as rows within a matrix.
T-Coffee (Tree-based Consistency Objective Function for Alignment Evaluation) is a multiple sequence alignment software using a progressive approach. [1] It generates a library of pairwise alignments to guide the multiple sequence alignment.
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
The frame used was frame 1 for the DNA sequence. As shown in the picture, there was a gap of 2 amino acids (6 nucleic acids) in the alignment, which results the total low score of -2. Figure 2 illustrates the aligned result using PairWise. Using the same DNA and protein sequence, and with the penalties modified as below.
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
BLAT (BLAST-like alignment tool) is a pairwise sequence alignment algorithm that was developed by Jim Kent at the University of California Santa Cruz (UCSC) in the early 2000s to assist in the assembly and annotation of the human genome. [1]
In bioinformatics and proteomics, ProbCons is an open source software for probabilistic consistency-based multiple alignment of amino acid sequences. It is one of the most efficient protein multiple sequence alignment programs, since it has repeatedly demonstrated a statistically significant advantage in accuracy over similar tools, including Clustal and MAFFT.