What is an Entrez Search

Sequence similarity search with the help of the "Basic Local Alignment Search Tool" (BLAST) in the sequence databases of the NCBI

Researching the Life Sciences pp 79-112 | Cite as

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abstract

Important information for the characterization of the unknown sequence can be obtained via a sequence similarity between an unknown and an already described sequence. In this way, gene and protein functions can be derived from a sequence similarity, conserved regions and domains can be identified in a sequence or vector sequences of a cloning plasmid can be found and eliminated. This chapter deals with database searches in the sequence databases, which were also discussed in the previous chapters, such as GenBank, RefSeq and Swiss-Prot. However, it does not treat the search query with keywords, but rather the search query with a sequence as a starting point. Various algorithms have been developed for a sequence similarity search. The most widely used search algorithm is integrated in BLAST, the "Basic Local Alignment Search Tool", and was published in 1990 by Stephen F. Altschul (American mathematician) initially for a comparison of protein sequences. The strengths of BLAST are the fast sequence comparison and the exact calculation of the statistical significance of the sequence similarity. The BLAST algorithm combines high sensitivity with very good selectivity. BLAST rarely calculates the values ​​for non-similar sequences, unless the sequence contains regions of low complexity. BLAST scores have statistical significance and real hits can be distinguished from background results.

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