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Fig. 2 The process to extend the exact match. Adapted from Biological Sequence Analysis I, Current Topics in Genome Analysis . Fig. 3 The positions of the exact matches. To save more time, a newer version of BLAST, called BLAST2 or gapped BLAST, has been developed.
BLAT (BLAST-like alignment tool) is a pairwise sequence alignment algorithm that was developed by Jim Kent at the University of California Santa Cruz (UCSC) in the early 2000s to assist in the assembly and annotation of the human genome. [1]
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.
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.
Search results are displayed in table format; from here the user may obtain further information about a particular database entry, or launch a VOCs-linked tool (see below) for analysis of selected data. Additional analysis tools such as BLAST searches, genome maps, genome or gene alignment, phylogenetic trees, etc. are provided. [5]
Local and NCBI Genbank BLAST search; Open reading frame finder; Restriction enzyme finder with integrated REBASE [5] restriction enzymes list; Integrated Primer3 package [6] for PCR primer design; Plasmid construction and annotation; Cloning in silico by designing of cloning vectors; Genome mapping of short reads with Bowtie, BWA, [7] and UGENE ...
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