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Literature DB >> 12125818

A simple sensitive program for detecting internal repeats in sets of multiply aligned homologous proteins.

Abstract

We designed a simple but sensitive program, IntraCompare, for identifying internal repeats in families of homologous proteins. The protein sequences are aligned (Clustal X), the regions to be compared are selected, and all potential repeat sequences are compared with all others. The output provides comparison scores (GAP program) expressed in standard deviations.

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Year: 2002 PMID： 12125818

Source DB: PubMed Journal: J Mol Microbiol Biotechnol ISSN： 1464-1801

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Cited

15 in total

1. Bioinformatic characterization of the trimeric intracellular cation-specific channel protein family.

Authors: Abe L F Silverio; Milton H Saier
Journal: J Membr Biol Date: 2011-04-26 Impact factor: 1.843

Review 2. Gap junctional proteins of animals: the innexin/pannexin superfamily.

Authors: Ming Ren Yen; Milton H Saier
Journal: Prog Biophys Mol Biol Date: 2007-03-15 Impact factor: 3.667

Review 3. Bioinformatic analyses of transmembrane transport: novel software for deducing protein phylogeny, topology, and evolution.

Authors: Ming Ren Yen; Jeehye Choi; Milton H Saier
Journal: J Mol Microbiol Biotechnol Date: 2009-09-18

4. Bioinformatic characterization of the 4-Toluene Sulfonate Uptake Permease (TSUP) family of transmembrane proteins.

Authors: Maksim A Shlykov; Wei Hao Zheng; Jonathan S Chen; Milton H Saier
Journal: Biochim Biophys Acta Date: 2011-12-13

5. Topological and phylogenetic analyses of bacterial holin families and superfamilies.

Authors: Bhaskara L Reddy; Milton H Saier
Journal: Biochim Biophys Acta Date: 2013-07-13

6. Animal Ca2+ release-activated Ca2+ (CRAC) channels appear to be homologous to and derived from the ubiquitous cation diffusion facilitators.

Authors: Madeleine G Matias; Kenny M Gomolplitinant; Dorjee G Tamang; Milton H Saier
Journal: BMC Res Notes Date: 2010-06-03

A simple sensitive program for detecting internal repeats in sets of multiply aligned homologous proteins.

1. Bioinformatic characterization of the trimeric intracellular cation-specific channel protein family.

Review 2. Gap junctional proteins of animals: the innexin/pannexin superfamily.

Review 3. Bioinformatic analyses of transmembrane transport: novel software for deducing protein phylogeny, topology, and evolution.

4. Bioinformatic characterization of the 4-Toluene Sulfonate Uptake Permease (TSUP) family of transmembrane proteins.

5. Topological and phylogenetic analyses of bacterial holin families and superfamilies.

6. Animal Ca2+ release-activated Ca2+ (CRAC) channels appear to be homologous to and derived from the ubiquitous cation diffusion facilitators.

7. Defense against cannibalism: the SdpI family of bacterial immunity/signal transduction proteins.

8. BioV Suite--a collection of programs for the study of transport protein evolution.

9. The Transporter Classification Database: recent advances.

10. State-dependent block of Na+ channels by articaine via the local anesthetic receptor.