Oxford Index Search Results

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PSI-BLAST

Overview page. Subjects: Chemistry.

abbr. for position‐specific iterated‐BLAST; see database‐search program.

See overview in Oxford Index

Powerful fusion: PSI-BLAST and consensus sequences

Dariusz Przybylski and Burkhard Rost.

in Bioinformatics

September 2008; p ublished online August 2008 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 4354 words.

Motivation: A typical PSI-BLAST search consists of iterative scanning and alignment of a large sequence database during which a scoring profile is progressively built and...

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BeoBLAST: distributed BLAST and PSI-BLAST on a Beowulf cluster

J. D. Grant, R. L. Dunbrack, F. J. Manion and M. F. Ochs.

in Bioinformatics

May 2002; p ublished online May 2002 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 0 words.

Summary: BeoBLAST is an integrated software package that handles user requests and distributes BLAST and PSI-BLAST searches to nodes of a Beowulf cluster, thus providing a simple way to...

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A performance enhanced PSI-BLAST based on hybrid alignment

Yuheng Li, Nicholas Chia, Mario Lauria and Ralf Bundschuh.

in Bioinformatics

January 2011; p ublished online November 2010 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 5958 words.

Motivation: Sequence alignment is one of the most popular tools of modern biology. NCBI's PSI-BLAST utilizes iterative model building in order to better detect distant homologs...

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Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

Stephen F. Altschul, Thomas L. Madden, Alejandro A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb Miller and David J. Lipman.

in Nucleic Acids Research

September 1997; p ublished online September 1997 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 10082 words.

The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical...

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PSI-BLAST pseudocounts and the minimum description length principle

Stephen F. Altschul, E. Michael Gertz, Richa Agarwala, Alejandro A. Schäffer and Yi-Kuo Yu.

in Nucleic Acids Research

February 2009; p ublished online December 2008 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 7595 words.

Position specific score matrices (PSSMs) are derived from multiple sequence alignments to aid in the recognition of distant protein sequence relationships. The PSI-BLAST protein database...

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Cascade PSI-BLAST web server: a remote homology search tool for relating protein domains

R. Bhadra, S. Sandhya, K. R. Abhinandan, S. Chakrabarti, R. Sowdhamini and N. Srinivasan.

in Nucleic Acids Research

July 2006; p ublished online July 2006 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 1912 words.

Owing to high evolutionary divergence, it is not always possible to identify distantly related protein domains by sequence search techniques. Intermediate sequences possess sequence features...

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PSIBLAST_PairwiseStatSig: reordering PSI-BLAST hits using pairwise statistical significance

Ankit Agrawal and Xiaoqiu Huang.

in Bioinformatics

April 2009; p ublished online February 2009 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 1196 words.

Summary: We present an add-on to BLAST and PSI-BLAST programs to reorder their hits using pairwise statistical significance. Using position-specific substitution matrices to...

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Consensus sequences improve PSI-BLAST through mimicking profile–profile alignments

Dariusz Przybylski and Burkhard Rost.

in Nucleic Acids Research

April 2007; p ublished online March 2007 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 6391 words.

Sequence alignments may be the most fundamental computational resource for molecular biology. The best methods that identify sequence relatedness through profile–profile comparisons are...

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SIB-BLAST: a web server for improved delineation of true and false positives in PSI-BLAST searches

Marianne M. Lee, Michael K. Chan and Ralf Bundschuh.

in Nucleic Acids Research

July 2009; p ublished online May 2009 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 2242 words.

A SIB-BLAST web server (http://sib-blast.osc.edu) has been established for investigators to use the SimpleIsBeautiful (SIB) algorithm for sequence-based homology detection. SIB was...

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HangOut: generating clean PSI-BLAST profiles for domains with long insertions

Bong-Hyun Kim, Qian Cong and Nick V. Grishin.

in Bioinformatics

June 2010; p ublished online April 2010 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 1481 words.

Summary: Profile-based similarity search is an essential step in structure-function studies of proteins. However, inclusion of non-homologous sequence segments into a profile...

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