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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]
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 ...
For example, if we had the amino acid sequences of proteins A and B and the amino acid sequences of all proteins in a certain genome, we could check each protein in that genome for non-overlapping regions of sequence similarity to both proteins A and B. Figure B depicts the BLAST sequence alignment of Succinyl coA Transferase with its two ...
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 ...
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 ...
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.
The deduced amino acid sequence can be saved in various formats and searched against the sequence database using the basic local alignment search tool (BLAST) server. The ORF Finder should be helpful in preparing complete and accurate sequence submissions. It is also packaged with the Sequin sequence submission software (sequence analyser).
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 .