BLAST program

The correct BLAST program for the analysis of nucleotide or amino acid sequences should be selected. A guide for BLAST program selection is available at http //www.ncbi.nlm.nih.gov/ BLAST/producttable.shtml. 

We cannot be sure of the answers provided by statistical methods. But if they are developed appropriately, they provide a significance estimate, such as the P-value that was the main claim to fame of the BLAST program and its real innovation. This value tells us how much we can believe an analysis or prediction, in the case of BLAST a local sequence match witnessed by an alignment. Recently several other bioinformatics analysis methods have been equipped with theoretically founded or heuristically fitted significance estimates (see Chapters 2 and 6 of Volume 1). Only few bioinformatics tools come with this kind of significance estimate today, and we need more of them. 

This BLAST Quickstart chapter illustrates the use of the principal BLAST programs to solve problems that arise in the analysis of protein and nucleotide sequences. Each section provides a succinct description of a protocol with two problems that serve as practical examples. Relevant theory is given when it affects the selection of a search strategy or search parameter, however, the emphasis is on the procedure itself. The sections follow closely the structure of the BLAST QuickStart Mini-Course found at www.ncbi.nlm.nih.gov/Class/minicourses. The BLAST QuickStart is one of 10 2-h format Mini-Courses offered by NCBI on campus at the National Institutes of Health and at locations around the country to over 4000 students a year. The courses use a paired problems approach in which the first of two similar problems or problem sets is solved by the instructor during the first hour on a computer linked to a projection system, while the students watch in the second hour, the students tackle the second problem, or set of problems at their... 

PSI-PRED [68,69] is a neural network-based program for predicting protein secondary structure query sequences are used as input to the PSI-BLAST program, whose (sequence profile) output forms the actual input to PSI-PRED. 

Sequence analysis. The GenBank database was searched using the NCBI BLAST program. Consensus sequences were generated and analysed using the programs of the DNASTAR. Multiple alignments of nucleotide were performed with the Clustal... 

The Basic Local Aligiunent Search Tool (BLAST Altschul et al., 1990) is a popular method of ascertaining sequence similarity. The BLAST program takes a query se-... 

Although not comprehensive as of this writing, SMART seems to be the most advanced of these systems, combining high sensitivity of domain detection with acciuacy, high speed, and extremely informative presentation of domain architectures. Rapid searches for protein domains, based on a modification of the PSl-BLAST program is now available through the Conserved Domains Database (CDD) at NCBI (cf. Chapter 11). 

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