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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 ...
Modern sensitive methods for protein search utilize sequence profiles. They may be used to compare a sequence to a profile, or in more advanced cases such as HH-suite, to match among profiles. [2] [6] [7] [8] Profiles and alignments are themselves derived from matches, using for example PSI-BLAST or HHblits.
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.
Software suite to search and cluster huge sequence sets. Similar sensitivity to BLAST and PSI-BLAST but orders of magnitude faster: Protein: Steinegger M, Mirdita M, Galiez C, Söding J [10] 2017 USEARCH Ultra-fast sequence analysis tool: Both: Edgar, R. C. (2010). "Search and clustering orders of magnitude faster than BLAST". Bioinformatics.
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
MNHN-Tree-Tools is an opensource phylogenetics inference software working on nucleic and protein sequences. Clustering of DNA or protein sequences and phylogenetic tree inference from a set of sequences. At the core it employs a distance-density based approach. Thomas Haschka, Loïc Ponger, Christophe Escudé and Julien Mozziconacci [28 ...
The BLAT Search Genome can accept multiple sequences of the same type at once, up to a maximum of 25. For multiple sequences, the total number of nucleotides must not exceed 50,000 for DNA searches or 25,000 letters for protein or translated sequence searches. An example of searching a target database with a DNA query sequence is shown in Figure 2.
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 .