PMID:15701682: Difference between revisions

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<span style = 'font-size: large'> '''Date, SV and Marcotte, EM'''  (2005) Protein function prediction using the Protein Link EXplorer (PLEX).''Bioinformatics'' '''21''':2558-9</span>
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|{{TableHeadingColor}} |'''Abstract''' || <protect>We introduce the Protein Link EXplorer (PLEX), a web-based environment that allows the construction of a phylogenetic profile for any given amino acid sequence, and its comparison with profiles of approximately 350,000 predicted genes from 89 genomes, as a means of interactively identifying functionally linked genes and predicting protein function. PLEX can be searched iteratively and also enables searches for chromosomal gene neighbors and Rosetta Stone linkages. PLEX search results are accompanied by quantitative estimates of linkage confidence, enabling users to take advantage of coinheritance, operon and gene fusion-based methods for inferring gene function and reconstructing cellular systems and pathways. AVAILABILITY: http://bioinformatics.icmb.utexas.edu/plex</protect>
!align=left  |Citation
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'''No author listed''' (2005) Protein function prediction using the Protein Link EXplorer (PLEX). ''Bioinformatics'' '''21''':2558-9
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!align=left  |Abstract
*  [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15701682 PubMed]
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We introduce the Protein Link EXplorer (PLEX), a web-based environment that allows the construction of a phylogenetic profile for any given amino acid sequence, and its comparison with profiles of approximately 350,000 predicted genes from 89 genomes, as a means of interactively identifying functionally linked genes and predicting protein function. PLEX can be searched iteratively and also enables searches for chromosomal gene neighbors and Rosetta Stone linkages. PLEX search results are accompanied by quantitative estimates of linkage confidence, enabling users to take advantage of coinheritance, operon and gene fusion-based methods for inferring gene function and reconstructing cellular systems and pathways. AVAILABILITY: http://bioinformatics.icmb.utexas.edu/plex
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!align=left  |Links
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15701682 PubMed]
Online version:[http://dx.doi.org/10.1093/bioinformatics/bti313 10.1093/bioinformatics/bti313]
Online version:[http://dx.doi.org/10.1093/bioinformatics/bti313 10.1093/bioinformatics/bti313]
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!align=left  |Keywords
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Algorithms; Amino Acid Sequence; Computer Graphics; Evolution, Molecular; Molecular Sequence Data; Phylogeny; Protein Conformation; Proteins/analysis; Proteins/chemistry; Proteins/metabolism; Sequence Alignment/methods; Sequence Analysis, Protein/methods; Sequence Homology, Amino Acid; Software; Structure-Activity Relationship; User-Computer Interface
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Revision as of 18:42, 1 September 2013

Citation

No author listed (2005) Protein function prediction using the Protein Link EXplorer (PLEX). Bioinformatics 21:2558-9

Abstract

We introduce the Protein Link EXplorer (PLEX), a web-based environment that allows the construction of a phylogenetic profile for any given amino acid sequence, and its comparison with profiles of approximately 350,000 predicted genes from 89 genomes, as a means of interactively identifying functionally linked genes and predicting protein function. PLEX can be searched iteratively and also enables searches for chromosomal gene neighbors and Rosetta Stone linkages. PLEX search results are accompanied by quantitative estimates of linkage confidence, enabling users to take advantage of coinheritance, operon and gene fusion-based methods for inferring gene function and reconstructing cellular systems and pathways. AVAILABILITY: http://bioinformatics.icmb.utexas.edu/plex

Links

PubMed Online version:10.1093/bioinformatics/bti313

Keywords

Algorithms; Amino Acid Sequence; Computer Graphics; Evolution, Molecular; Molecular Sequence Data; Phylogeny; Protein Conformation; Proteins/analysis; Proteins/chemistry; Proteins/metabolism; Sequence Alignment/methods; Sequence Analysis, Protein/methods; Sequence Homology, Amino Acid; Software; Structure-Activity Relationship; User-Computer Interface

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