A fast Peptide Match service for UniProt Knowledgebase.
- Chen C Center for Bioinformatics and Computational Biology and Protein Information Resource, University of Delaware, Newark, DE 19711, USA, Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK and Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1211 Geneva 4, Switzerland.
- Li Z
- Huang H
- Suzek BE
- Wu CH
- 2013-08-21
Published in:
- Bioinformatics (Oxford, England). - 2013
Databases, Protein
Internet
Knowledge Bases
Peptides
Proteomics
Search Engine
Sequence Analysis, Protein
English
SUMMARY
We have developed a new web application for peptide matching using Apache Lucene-based search engine. The Peptide Match service is designed to quickly retrieve all occurrences of a given query peptide from UniProt Knowledgebase (UniProtKB) with isoforms. The matched proteins are shown in summary tables with rich annotations, including matched sequence region(s) and links to corresponding proteins in a number of proteomic/peptide spectral databases. The results are grouped by taxonomy and can be browsed by organism, taxonomic group or taxonomy tree. The service supports queries where isobaric leucine and isoleucine are treated equivalent, and an option for searching UniRef100 representative sequences, as well as dynamic queries to major proteomic databases. In addition to the web interface, we also provide RESTful web services. The underlying data are updated every 4 weeks in accordance with the UniProt releases.
AVAILABILITY
http://proteininformationresource.org/peptide.shtml.
CONTACT
chenc@udel.edu.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
We have developed a new web application for peptide matching using Apache Lucene-based search engine. The Peptide Match service is designed to quickly retrieve all occurrences of a given query peptide from UniProt Knowledgebase (UniProtKB) with isoforms. The matched proteins are shown in summary tables with rich annotations, including matched sequence region(s) and links to corresponding proteins in a number of proteomic/peptide spectral databases. The results are grouped by taxonomy and can be browsed by organism, taxonomic group or taxonomy tree. The service supports queries where isobaric leucine and isoleucine are treated equivalent, and an option for searching UniRef100 representative sequences, as well as dynamic queries to major proteomic databases. In addition to the web interface, we also provide RESTful web services. The underlying data are updated every 4 weeks in accordance with the UniProt releases.
AVAILABILITY
http://proteininformationresource.org/peptide.shtml.
CONTACT
chenc@udel.edu.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
- Language
-
- English
- Open access status
- green
- Identifiers
-
- DOI 10.1093/bioinformatics/btt484
- PMID 23958731
- Persistent URL
- https://sonar.ch/global/documents/118177
Statistics
Document views: 38
File downloads:
- Full-text: 0