BLAST and BLAT - Algorithms in Bioinformatics

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22 Bioinformatics I, WS’12/13, D. Huson, October 30, 2012 3.3.4 Bit score The alignment score Z (also called raw score) is of little use without detailed knowledge of the substitution matrix and gap scoring scheme used, which are hidden in the statistical parameters K and λ. By factoring in the parameters K and λ, one obtains a normalized raw score called the bit score Z ′ , which is defined as Z ′ λS − ln K = . ln 2 If the bitscore Z ′ is known, then the E-value can easily be computed using the length of the two involved sequences: E = mn2 −Z′ . (Plug-in the definition of Z ′ to get back the original expression for E.) 3.4 Gapped BLAST A new version of BLAST called BLAST 2.0 2 allows gaps in the extension phase. 3.5 Different Flavors of BLAST BLAST programs: • BLASTN: compares a DNA query sequence to a DNA sequence database • BLASTP: compares a protein query sequence to a protein sequence database • TBLASTN: compares a protein query sequence to a DNA sequence database (6 frames translation) • BLASTX: compares a DNA query sequence (6 frames translation) to a protein sequence database • TBLASTX: compares a DNA query sequence (6 frames translation) to a DNA sequence database (6 frames translation) • Phi-BLAST: Pattern Hit Initiated BLAST searches for particular patterns in protein queries, incorp. into PSI-Blast • PSI-BLAST: Position specific iterated BLAST – profile of hits is computed – database is searched with profile – many iterations – designed to detect weak relationships between the query and members of the database not necessarily detectable by standard BLAST searches. – results in increased sensitivity 2 S. F. Altschul, T. L. Madden, A.A. Schäffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25(17):3389-402 (1997).
Bioinformatics I, WS’12/13, D. Huson, October 30, 2012 23 3.6 Available BLAST implementations Implementations: • NCBI BLAST: Implementation of all BLAST programs maintained by NCBI. • AB-BLAST (former WU-BLAST): Alternative implementation of all BLAST programs (except for PHI- and PSI-BLAST), needs a license (which costs money) • There are a number of commercial implementations of BLAST on GPUs and specialized hardware 3.7 BLAT BLAT = Blast Like Alignment Tool 3 BLAT is an alternative to BLAST that was developed in the context of the Human Genome Project. Its targets the comparison of genomes (e.g. human and mouse) or mRNA/DNA and cross-species protein alignments. Task that motivated development of BLAT: Map three million ESTs 4 (1.7 Gb) and 13 million whole gnome shotgun reads to a draft sequence of the human genome (2.88 Gb). 3.8 BLAT vs BLAST BLAT is similar to BLAST: The program rapidly scans for relatively short matches (hits) and extends these into HSPs. However BLAT differs from BLAST in some important ways: • BLAST builds an index of the query string and then scans linearly through the database – BLAT builds an index of the database and then scans linearly through the query, • BLAST triggers an extension when one or two hits occur – BLAT can trigger extensions on any given number of perfect or near perfect seed matches, • BLAST returns each area of homology as separate alignments – BLAT chains them together into larger alignments, • BLAST delivers a list of exons sorted by size, with alignments extending slightly beyond the edge of each exon – BLAT “unsplices” mRNA onto the genome, giving a single alignment that uses each base of the mRNA only once, with correctly positioned splice sites. 3.9 Sensitivity and Specificity Classifications: An “event” or “signal” (such as a DNA sequences is orthologous to a second one, a given DNA sequence is contained in a given coding region, or a gene is differentially expressed etc.) can • be predicted to occur: Predicted Positive • be predicted not to occur: Predicted Negative 3 W. J. Kent: BLAT - The BLAST-Like Alignment Tool. Genome Res. 12:656-664(2002) 4 An expressed sequence tag or EST is a short sub-sequence of a cDNA sequence used in the investigation of genes.
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