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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 ...
For multiple sequences the last row in each column is often the consensus sequence determined by the alignment; the consensus sequence is also often represented in graphical format with a sequence logo in which the size of each nucleotide or amino acid letter corresponds to its degree of conservation.
Search for ncRNAs in genomes by partition function local alignment: Nucleotide Sequerome: Profiling sequence alignment data with major servers/services: Nucleotide, peptide Sequilab Profiling sequence alignment data from NCBI-BLAST results with major servers-services: Nucleotide, peptide Shuffle-LAGAN Pairwise global alignment of completed ...
BLAT connects each homologous area between two sequences into a single larger alignment, in contrast to BLAST which returns each homologous area as a separate local alignment. The result of BLAST is a list of exons with each alignment extending just past the end of the exon. BLAT, however, correctly places each base of the mRNA onto the genome ...
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.
A scoring matrix or a table of values is required for evaluating the significance of a sequence alignment, such as describing the probability of a biologically meaningful amino-acid or nucleotide residue-pair occurring in an alignment. Typically, when two nucleotide sequences are being compared, all that is being scored is whether or not two ...
A profile HMM modelling a multiple sequence alignment. HMMER is a free and commonly used software package for sequence analysis written by Sean Eddy. [2] Its general usage is to identify homologous protein or nucleotide sequences, and to perform sequence alignments.
Sequence homology is the biological homology between DNA, RNA, or protein sequences, defined in terms of shared ancestry in the evolutionary history of life. Two segments of DNA can have shared ancestry because of three phenomena: either a speciation event (orthologs), or a duplication event (paralogs), or else a horizontal (or lateral) gene ...