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Peptide Match specifications

Information


Unique identifier OMICS_10130
Name Peptide Match
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Chenc

Information


Unique identifier OMICS_10130
Name Peptide Match
Interface Web user interface
Restrictions to use None
Programming languages Javascript
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Chenc

Publication for Peptide Match

Peptide Match citations

 (6)
library_books

Multilevel genomics of colorectal cancers with microsatellite instability—clinical impact of JAK1 mutations and consensus molecular subtype 1

2017
Genome Med
PMCID: 5442873
PMID: 28539123
DOI: 10.1186/s13073-017-0434-0

[…] filtered to exclude peptides encoded from other, non-mutated loci in the human genome by searching for perfect matches of the peptide sequences in UniProtKB release 2015_11 using the web application Peptide Match service for UniProt Knowledgebase []. Lastly, to include only peptides predicted to be generated by cleavage in proteasomes, the list of neoantigens was filtered to include only peptides […]

library_books

From Toxoplasmosis to Schizophrenia via NMDA Dysfunction: Peptide Overlap between Toxoplasma gondii and N Methyl d Aspartate Receptors As a Potential Mechanistic Link

2017
PMCID: 5350139
PMID: 28360866
DOI: 10.3389/fpsyt.2017.00037

[…] uced a library consisting of 8,578 NMDAR subunit hexapeptides. Each NMDAR hexapeptide was used as a probe to search the entire T. gondii proteome for occurrences of the same hexapeptide using the Pir Peptide Match program ().Toxoplasma gondii (strain VEG, NCBI Tax ID: 432359) was investigated. The T. gondii proteome consists of 8,404 proteins (Uniprot proteome: UP000002226). The protozoan Entamoeb […]

library_books

The Widespread Prevalence and Functional Significance of Silk Like Structural Proteins in Metazoan Biological Materials

2016
PLoS One
PMCID: 4944945
PMID: 27415783
DOI: 10.1371/journal.pone.0159128

[…] , all silk-like proteins from S. purpuratus were assembled into a database and queried for peptide sequences previously isolated from spicule, test, spines and teeth [–] using a local installation of Peptide Match []. Default settings were used, and leucine and isoleucine were not treated as equivalent. […]

library_books

Lepidopteran defence droplets a composite physical and chemical weapon against potential predators

2016
Sci Rep
PMCID: 4778013
PMID: 26940001
DOI: 10.1038/srep22407

[…] icates that the peptide in Z. filipendulae originates via post translational processing. To find a possible match for the peptide in other organisms, the sequence was searched against UniProtKB using Peptide Match and against the NCBI non-redundant protein sequences database using the BLASTP algorithm. This approach resulted in sequence hits from several different organisms with 100% coverage and […]

library_books

Validation, optimisation, and application data in support of the development of a targeted selected ion monitoring assay for degraded cardiac troponin T

2016
PMCID: 4782000
PMID: 26977445
DOI: 10.1016/j.dib.2016.02.051

[…] The specificity of each targeted peptide for cTnT was verified by performing a sequence identity search of all included peptides using the peptide match tool of the online Protein Information Resource (PIR, http://research.bioinformatics.udel.edu/peptidematch/index.jsp) , . The database that was searched was the complete, unrestricted, U […]

library_books

Mass Spectrometry Offers Insight into the Role of Ser/Thr/Tyr Phosphorylation in the Mycobacteria

2016
Front Microbiol
PMCID: 4751927
PMID: 26904014
DOI: 10.3389/fmicb.2016.00141

[…] published supplementary information. To facilitate comparison at the protein level, the peptide sequences were matched to H37Rv protein identifiers using the Protein Information Resource (PIR) batch peptide match tool against the Uniprot H37Rv proteome (Chen et al., ). GO analysis of the proteins corresponding to these shared phosphopeptides using STRAP 1.5 (Bhatia et al., ) revealed that the ass […]


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Peptide Match institution(s)
Center for Bioinformatics and Computational Biology and Protein Information Resource, University of Delaware, Newark, DE, USA; Protein Information Resource, Georgetown University Medical Center, WA, DC, USA; European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK; Swiss Institute of Bioinformatics, Centre Medical Universitaire, Geneva, Switzerland
Peptide Match funding source(s)
NIH (1U41HG006104-03) and Institutional Resources at University of Delaware

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