Basic Local Alignment Search Tool (BLAST) Algorithm

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A Basic Local Alignment Search Tool (BLAST) Algorithm is a sequence alignment algorithm for searching sequence databases.



References

2021a

2021b

2021c

  • (Wikipedia, 2021) ⇒ https://en.wikipedia.org/wiki/BLAST_(biotechnology) Retrieved:2021-2-25.
    • In bioinformatics, BLAST (basic local alignment search tool) 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) with a library or database of sequences, and identify database sequences that resemble the query sequence above a certain threshold. For example, following the discovery of a previously unknown gene in the mouse, a scientist will typically perform a BLAST search of the human genome to see if humans carry a similar gene; BLAST will identify sequences in the human genomethat resemble the mouse gene based on similarity of sequence.

2020

(...) For more about the optional BLAST arguments, we refer you to the NCBI’s own documentation, or that built into Biopython:
>>> from Bio. Blast import NCBIWWW
>>> help(NCBIWWW.qblast)
...
Note that the default settings on the NCBI BLAST website are not quite the same as the defaults on QBLAST. If you get different results, you’ll need to check the parameters (e.g., the expectation value threshold and the gap values).

For example, if you have a nucleotide sequence you want to search against the nucleotide database (nt) using BLASTN, and you know the GI number of your query sequence, you can use:

>>> from Bio. Blast import NCBIWWW
>>> result_handle = NCBIWWW.qblast("blastn", "nt", "8332116")

2009

  • (NCBI, 2009) ⇒ http://blast.ncbi.nlm.nih.gov/Blast.cgi
    • The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

2009b

1990

1981