Please use this identifier to cite or link to this item: http://hdl.handle.net/1822/46331

TitleP4P: a peptidome-based strain-level genome comparison web tool
Author(s)Blanco-Míguez, Aitor
Fdez-Riverola, Florentino
Lourenço, Anália
Sánchez, Borja
Issue date2017
PublisherOxford University Press
JournalNucleic Acids Research
CitationBlanco-Míguez, Aitor; Fdez-Riverola, Florentino; Lourenço, Anália; Sánchez, Borja, P4P: a peptidome-based strain-level genome comparison web tool. Nucleic Acids Research, 45(W1), W265-W269, 2017
Abstract(s)Peptidome similarity analysis enables researchers to gain insights into differential peptide profiles, providing a robust tool to discriminate strain-specific peptides, true intra-species differences among biological replicates or even microorganism-phenotype variations. However, no in silico peptide fingerprinting software existed to facilitate such phylogeny inference. Hence, we developed the Peptidomes for Phylogenies (P4P) web tool, which enables the survey of similarities between microbial proteomes and simplifies the process of obtaining new biological insights into their phylogeny. P4P can be used to analyze different peptide datasets, i.e. bacteria, viruses, eukaryotic species or even metaproteomes. Also, it is able to work with whole proteome datasets and experimental mass-to-charge lists originated from mass spectrometers. The ultimate aim is to generate a valid and manageable list of peptides that have phylogenetic signal and are potentially sample-specific. Sample-to-sample comparison is based on a consensus peak set matrix, which can be further submitted to phylogenetic analysis. P4P holds great potential for improving phylogenetic analyses in challenging taxonomic groups, biomarker identification or epidemiologic studies. Notably, P4P can be of interest for applications handling large proteomic datasets, which it is able to reduce to small matrices while maintaining high phylogenetic resolution. The web server is available at http://sing-group.org/p4p.
TypeArticle
URIhttp://hdl.handle.net/1822/46331
DOI10.1093/nar/gkx389
ISSN0305-1048
e-ISSN1362-4962
Publisher versionhttp://nar.oxfordjournals.org/
Peer-Reviewedyes
AccessOpen access
Appears in Collections:CEB - Publicações em Revistas/Séries Internacionais / Publications in International Journals/Series

Files in This Item:
File Description SizeFormat 
document_46896_1.pdf670,51 kBAdobe PDFView/Open

Partilhe no FacebookPartilhe no TwitterPartilhe no DeliciousPartilhe no LinkedInPartilhe no DiggAdicionar ao Google BookmarksPartilhe no MySpacePartilhe no Orkut
Exporte no formato BibTex mendeley Exporte no formato Endnote Adicione ao seu ORCID