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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 ...
A consensus logo is a simplified variation of a sequence logo that can be embedded in text format. Like a sequence logo, a consensus logo is created from a collection of aligned protein or DNA/RNA sequences and conveys information about the conservation of each position of a sequence motif or sequence alignment [1] [4].
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.
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 main diagonal represents the sequence's alignment with itself; lines off the main diagonal represent similar or repetitive patterns within the sequence. In bioinformatics a dot plot is a graphical method for comparing two biological sequences and identifying regions of close similarity after sequence alignment. It is a type of recurrence plot.
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 ...
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 ...
BLAT can be used to align DNA sequences as well as protein and translated nucleotide (mRNA or DNA) sequences. It is designed to work best on sequences with great similarity. The DNA search is most effective for primates and the protein search is effective for land vertebrates.