Databases BLAST search

It is also possible to extend this concept to cover the presence of more than one distinct segm pair in a pair of sequences (for example, if there are three MSPs present with scores of 40, and 50 then one can calculate the probabOity of finding three pairs with at least a score of by chance). The ability of BLAST to provide a quantitative significance of any match fou is a particularly useful feature of the program, which, with its continuing development a availability, has made it the most widely used method for sequence database searching. 

Altschul S F, T L Madden, A A Schaffer, J Zhang, Z Zhang, W Miller and D J Lipman 1997. Gapped BLAST and PSI-BLAST A New Generation of Protein Database Search Programs. Nucleic Acids Research 25 3389-3402. 

Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ, Gapped BLAST and PSI-BLAST a new generation of protein database search programs. Nucleic Acids Res 1997 25 3389-402. 

PSI-BLAST (Altschul et al., 1997) is rapidly becoming the tool of choice for protein database searching because of its speed, sensitivity and ease of use. It presents a very large improvement over the older versions of BLAST and new gapped-BLAST implementations (Altschul et al., 1997 Altschul et al., 1990). However, a naive user can easily be misled or not get the best possible results. PSI-BLAST is available as a stand-alone program from ftp //and as an interactive web tool at http //www.ncbi. nlm.nih.gov/cgibin/BLAST/nph-psi blast... 

Multiple alignments of repeats are constructed in an iterative manner. The initial alignment is based on definitions from determined protein structures or else from the literature. In the initial database search step, a profile constructed from the multiple alignment is compared with a sequence database. Top scoring sequences are considered using complementary approaches such as PSI-BLAST and FASTA to provide the two thresholds minimum E value and minimum number of repeats per protein required. After one or two iterations, the final alignment and the thresholds are stored in the SMART database to allow the detection of repeats in any sequence. 

Altschul, S., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. (1997). Gapped BLAST anmd PSI-BLAST a new generation of protein database search programs. Nucl. Adds Res. 25, 3389-3402. 

BLAST Chime Entrez (NCBI) FASTA GenBank (NCBI) Molecules R Us RasMol (Ras Mac) SRS (EMBL) Searches for similar protein and nucleic acid sequences Protein structures on moving 3D coordinates Sequence retrieval system for cross-referencing databases Searches for similar protein sequences Database of gene sequences Provides coordinates for protein 3D structure and manipulation Provides coordinates for protein 3D structure and manipulation Sequence retrieval system for cross referencing databases... 

All of the three IC centers also provide facilities for sequence similarity search and alignment. The widely used database search algorithms are FASTA (Lipman and Pearson, 1985) at http //www.nbrf.georgetown.edu/pirwww/search/fasta.html and BLAST (Altschul et al., 1990) at http //www.ncbi.nlm.nih.gov/BLAST/. For BLAST... 

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