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Basic local alignment search tools

Altschul S F, W Gish, W Miller, E W Myers and D J Lipman 1990. Basic Local Alignment Search Tool. Journal of Molecular Biology 215 403-410. [Pg.574]

SF Altschul, W Gish, W Miller, EW Myers, DJ Lipman. Basic local alignment search tool. J Mol Biol 215 403-410, 1990. [Pg.303]

The aim of the fust dimension breadth is to reveal sequence-function relationships by comparing protein sequences by sequence similarity. Simple bioinformatic algorithms can be used to compare a pair of related proteins or for sequence similarity searches e.g., BLAST (Basic Local Alignment Search Tool). Improved algorithms allow multiple alignments of larger number of proteins and extraction of consensus sequence pattern and sequence profiles or structural templates, which can be related to some functions, see e.g., under http //www. expasy.ch/tools/ similarity. [Pg.777]

BLAST basic local alignment search tool... [Pg.418]

Sequence similarity searching Basic Local Alignment Search Tool (BLAST) http //www.ncbi.nlm.nih.gov/BLAST/ Comparison of novel sequences with known genes. [Pg.8]

Ahting U et al. (1999) The TOM core complex the general protein import pore of the outer membrane of mitochondria. J Cell Biol 147 959-968 Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215 403-410... [Pg.62]

A sequence alignment is a way of determining the similarity between two strings. This is a classical question in computer science, and has an exact solution referred to as the Smith/Waterman alignment. Unfortunately, this exact solution can be slow when analyzing large sequences, and therefore, approximate methods, such as Basic Local Alignment Search Tool (BLAST), have been developed to identify very similar sequences. [Pg.517]

The potential for autoimmunity should be considered when cells are used for immunotherapy purposes [52], The basic local alignment search tool... [Pg.770]

BLAST Basic Local Alignment Search Tool. One of the more widely used tools in genome informatics, for similarity searches of protein or DNA sequences. [Pg.163]

The most popular tool currently in use is BLAST (Basic Local Alignment Search Tool) (3 7) from the NCBI. BLAST is an example of a heuristic that attempts to optimize a specific similarity measure. The most recent revisions to the algorithm are gapped BLAST and PSI-BLAST (38), with improved accuracy for PSI-BLAST using composition-based statistics... [Pg.347]

Therefore, and also to compare the results with existing information, one may still want to search the database with the results obtained by de novo sequencing. The approach to follow is a BLAST search (Basic Local Alignment Search Tool, [133-134]). Sequence alignment is a powerful way to compare novel sequences with previously characterized sequences and search for similarities. The BLAST search is much slower than the database searches outlined in Ch. 17.6.2. A nice example is the de novo identification of the bacterium Shewanella putrefaciens proteome by 2D-GE, in-gel digestion, direct infusion nano-ESl, and nano-LC-MS [135]. The results were BLAST searched against the incomplete genome of the bacterium. [Pg.478]

BLAST Basic Local Alignment Search Tool... [Pg.614]

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See also in sourсe #XX -- [ Pg.3151 ]

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See also in sourсe #XX -- [ Pg.212 ]

See also in sourсe #XX -- [ Pg.11 ]



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