PTM-Logo: a program for generation of sequence logos based on position-specific background amino-acid probabilities.
Journal
Bioinformatics (Oxford, England)
ISSN: 1367-4811
Titre abrégé: Bioinformatics
Pays: England
ID NLM: 9808944
Informations de publication
Date de publication:
15 12 2019
15 12 2019
Historique:
received:
01
03
2019
revised:
29
05
2019
accepted:
16
07
2019
pubmed:
19
7
2019
medline:
8
7
2020
entrez:
19
7
2019
Statut:
ppublish
Résumé
Identification of the amino-acid motifs in proteins that are targeted for post-translational modifications (PTMs) is of great importance in understanding regulatory networks. Information about targeted motifs can be derived from mass spectrometry data that identify peptides containing specific PTMs such as phosphorylation, ubiquitylation and acetylation. Comparison of input data against a standardized 'background' set allows identification of over- and under-represented amino acids surrounding the modified site. Conventionally, calculation of targeted motifs assumes a random background distribution of amino acids surrounding the modified position. However, we show that probabilities of amino acids depend on (i) the type of the modification and (ii) their positions relative to the modified site. Thus, software that identifies such over- and under-represented amino acids should make appropriate adjustments for these effects. Here we present a new program, PTM-Logo, that generates representations of these amino acid preferences ('logos') based on position-specific amino-acid probability backgrounds calculated either from user-input data or curated databases. PTM-Logo is freely available online at http://sysbio.chula.ac.th/PTMLogo/ or https://hpcwebapps.cit.nih.gov/PTMLogo/. Supplementary data are available at Bioinformatics online.
Identifiants
pubmed: 31318409
pii: 5535597
doi: 10.1093/bioinformatics/btz568
pmc: PMC7500089
doi:
Substances chimiques
Amino Acids
0
Proteins
0
Types de publication
Journal Article
Research Support, N.I.H., Intramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
5313-5314Subventions
Organisme : Intramural NIH HHS
ID : Z01 HL001285
Pays : United States
Informations de copyright
© The Author(s) 2019. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
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