Pclust: Protein network visualization highlighting experimental data

Wenlin Li, Lisa N. Kinch, Nick V. Grishin

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

Summary: One approach to infer functions of new proteins from their homologs utilizes visualization of an all-against-all pairwise similarity network (A2ApsN) that exploits the speed of BLAST and avoids the complexity of multiple sequence alignment. However, identifying functions of the protein clusters in A2ApsN is never trivial, due to a lack of linking characterized proteins to their relevant information in current software packages. Given the database errors introduced by automatic annotation transfer, functional deduction should be made from proteins with experimental studies, i.e. 'reference proteins'. Here, we present a web server, termed Pclust, which provides a user-friendly interface to visualize the A2ApsN, placing emphasis on such 'reference proteins' and providing access to their full information in source databases, e.g. articles in PubMed. The identification of 'reference proteins' and the ease of cross-database linkage will facilitate understanding the functions of protein clusters in the network, thus promoting interpretation of proteins of interest. Availability: The Pclust server is freely available at http://prodata.swmed.edu/pclust Contact: grishin@chop.swmed.edu Supplementary Information: Supplementary data are available at Bioinformatics online.

Original languageEnglish (US)
Pages (from-to)2647-2648
Number of pages2
JournalBioinformatics
Volume29
Issue number20
DOIs
StatePublished - Oct 15 2013

Fingerprint

Visualization
Experimental Data
Proteins
Protein
Databases
Servers
Multiple Sequence Alignment
Sequence Alignment
Web Server
Deduction
Bioinformatics
Computational Biology
PubMed
Software Package
Software packages
Linkage
User Interface
User interfaces
Linking
Annotation

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computational Theory and Mathematics
  • Computer Science Applications
  • Computational Mathematics
  • Statistics and Probability
  • Medicine(all)

Cite this

Pclust : Protein network visualization highlighting experimental data. / Li, Wenlin; Kinch, Lisa N.; Grishin, Nick V.

In: Bioinformatics, Vol. 29, No. 20, 15.10.2013, p. 2647-2648.

Research output: Contribution to journalArticle

Li, Wenlin ; Kinch, Lisa N. ; Grishin, Nick V. / Pclust : Protein network visualization highlighting experimental data. In: Bioinformatics. 2013 ; Vol. 29, No. 20. pp. 2647-2648.
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