Sequence similarity is a powerful tool for discovering biological function. Just as the ancient Greeks used comparative anatomy to understand the human body and linguists used the Rosetta stone to decipher Egyptian hieroglyphs, today we can use comparative sequence analysis to understand genomes. BLAST (Basic Local Alignment Search Tool), is a sophisticated software package for rapid searching of nucleotide and protein databases. It is one of the most important software packages used in sequence analysis and bioinformatics. Most users of BLAST, however, seldom move beyond the program's default parameters, and never take advantage of its full power. BLAST is the only book completely devoted to this popular suite of tools. It offers biologists, computational biology students, and bioinformatics professionals a clear understanding of BLAST as well as the science it supports. This book shows you how to move beyond the default parameters, get specific answers using BLAST, and how to interpret your results. The book also contains tutorial and reference sections covering NCBI-BLAST and WU-BLAST, background material to help you understand the statistics behind BLAST, Perl scripts to help you prepare your data and analyze your results, and a wealth of tips and tricks for configuring BLAST to meet your own research needs. Some of the topics covered include:
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accession number algorithm alias database amino acid biological Bioperl bit score bl2seq BLAST databases BLAST report BLAST search blastpgp BLOSUM62 Book Caenorhabditis elegans Caenorhabditis elegans cDNA calculate Chapter cluster coding coelacanth command line contains database sequences definition line effective length eMatter Edition Equation ESTs eukaryotes example exons Expect FASTA file FASTA format fastacmd Figure format formatdb gap penalties gapped alignments GenBank genes genomic sequence globins hits identifiers indexing integer introns Karlin-Altschul statistics lambda letters low-complexity match megablast mismatch molecular mRNA mutation nats NCBI nucleotide nucleotide sequences oligo Optimizations option output P-value percent identity Perl pseudogenes PSI-BLAST query sequence query-anchored raw score regions retrieve Sbjct Score Score Score scoring matrix scoring scheme search space seeding sensitivity sequence database similar stop codons strand sum score target frequency threshold Title transcripts Unix users word word size WU-BLAST xdformat xdget