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Literature DB >> 23749753

An introduction to sequence similarity ("homology") searching.

Abstract

Sequence similarity searching, typically with BLAST, is the most widely used and most reliable strategy for characterizing newly determined sequences. Sequence similarity searches can identify "homologous" proteins or genes by detecting excess similarity- statistically significant similarity that reflects common ancestry. This unit provides an overview of the inference of homology from significant similarity, and introduces other units in this chapter that provide more details on effective strategies for identifying homologs.

Entities: Disease Gene Species

Mesh：

Substances：
Proteins

Year: 2013 PMID： 23749753 PMCID： PMC3820096 DOI： 10.1002/0471250953.bi0301s42

Source DB: PubMed Journal: Curr Protoc Bioinformatics ISSN： 1934-3396

12 in total

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2. MUSCLE: multiple sequence alignment with high accuracy and high throughput.

Authors: Robert C Edgar
Journal: Nucleic Acids Res Date: 2004-03-19 Impact factor: 16.971

Review 3. Orthologs, paralogs, and evolutionary genomics.

Authors: Eugene V Koonin
Journal: Annu Rev Genet Date: 2005 Impact factor: 16.830

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Authors: M A Larkin; G Blackshields; N P Brown; R Chenna; P A McGettigan; H McWilliam; F Valentin; I M Wallace; A Wilm; R Lopez; J D Thompson; T J Gibson; D G Higgins
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Review 5. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

Authors: S F Altschul; T L Madden; A A Schäffer; J Zhang; Z Zhang; W Miller; D J Lipman
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6. Identification of common molecular subsequences.

Authors: T F Smith; M S Waterman
Journal: J Mol Biol Date: 1981-03-25 Impact factor: 5.469

7. Searching protein sequence libraries: comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms.

Authors: W R Pearson
Journal: Genomics Date: 1991-11 Impact factor: 5.736

8. PSI-Search: iterative HOE-reduced profile SSEARCH searching.

Authors: Weizhong Li; Hamish McWilliam; Mickael Goujon; Andrew Cowley; Rodrigo Lopez; William R Pearson
Journal: Bioinformatics Date: 2012-04-25 Impact factor: 6.937

Review 9. Can sequence determine function?

Authors: J A Gerlt; P C Babbitt
Journal: Genome Biol Date: 2000-11-08 Impact factor: 13.583

10. Homologous over-extension: a challenge for iterative similarity searches.

Authors: Mileidy W Gonzalez; William R Pearson
Journal: Nucleic Acids Res Date: 2010-01-11 Impact factor: 16.971

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