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BLAT can extend on multiple perfect and near-perfect matches (default is 2 perfect matches of length 11 for nucleotide searches and 3 perfect matches of length 4 for protein searches), while BLAST extends only when one or two matches occur close together. [1] [9] BLAT connects each homologous area between two sequences
On the other hand, the program XNU is used to mask off the tandem repeats in protein sequences. Make a k-letter word list of the query sequence. Take k=3 for example, we list the words of length 3 in the query protein sequence (k is usually 11 for a DNA sequence) "sequentially", until the last letter of the query sequence is included. The ...
An example of this is the Human Succinyl coA Transferase enzyme, which is found as one protein in humans but as two separate proteins, Acetate coA Transferase alpha and Acetate coA Transferase beta, in Escherichia coli. [3] In order to identify these sequences, a sequence similarity algorithm such as the one used by BLAST is necessary.
A part of a multiple sequence alignment of four different hemoglobin protein sequences. Similar protein sequences, usually indicate shared functions. Proteins of similar sequence are usually homologous [5] and thus have a similar function. Hence proteins in a newly sequenced genome are routinely annotated using the sequences of similar proteins ...
It makes use of the BLAST [5] algorithm to identify similar sequences to then transfers existing functional annotation from yet characterised sequences to the novel one. The functional information is represented via the Gene Ontology (GO), a controlled vocabulary of functional attributes.
After all sequences are searched the program plots the initial scores of each database sequence in a histogram, and calculates the statistical significance of the "opt" score. For protein sequences, the final alignment is produced using a full Smith–Waterman alignment. For DNA sequences, a banded alignment is provided.
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.
Multiple sequence alignment (MSA) is the process or the result of sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. These alignments are used to infer evolutionary relationships via phylogenetic analysis and can highlight homologous features between sequences.