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In bioinformatics, BLAST (basic local alignment search tool) [3] is an algorithm and program for comparing primary biological sequence information, such as the amino-acid sequences of proteins or the nucleotides of DNA and/or RNA sequences. A BLAST search enables a researcher to compare a subject protein or nucleotide sequence (called a query ...
One way to visualize the similarity between two protein or nucleic acid sequences is to use a similarity matrix, known as a dot plot. These were introduced by Gibbs and McIntyre in 1970 [1] and are two-dimensional matrices that have the sequences of the proteins being compared along the vertical and horizontal axes.
Alignments for membrane protein sequences: Protein: Both: M. Stamm, K. Khafizov, R. Staritzbichler, L.R. Forrest: 2013 ALLALIGN For DNA, RNA and protein molecules up to 32MB, aligns all sequences of size K or greater. Similar alignments are grouped together for analysis. Automatic repetitive sequence filter. Both Local E. Wachtel 2017
BLAT can be used for alignments of two protein sequences. However, it is not the tool of choice for these types of alignments. BLASTP, the Standard Protein BLAST tool, is more efficient at protein-protein alignments; [1] Determination of the distribution of exonic and intronic regions of a gene; [9] [10]
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
One would use a higher numbered BLOSUM matrix for aligning two closely related sequences and a lower number for more divergent sequences. It turns out that the BLOSUM62 matrix does an excellent job detecting similarities in distant sequences, and this is the matrix used by default in most recent alignment applications such as BLAST .
CS-BLAST greatly improves alignment quality over the entire range of sequence identities and especially for difficult alignments in comparison to regular BLAST and PSI-BLAST. PSI-BLAST (Position-Specific Iterated BLAST) runs at about the same speed per iteration as regular BLAST, but is able to detect weaker sequence similarities that are still ...
For instance, two protein sequences may be relatively similar but differ at certain intervals as one protein may have a different subunit compared to the other. Representing these differing sub-sequences as gaps will allow us to treat these cases as “good matches” even though there are long consecutive runs with indel operations in the ...