REP2: A Web Server to Detect Common Tandem Repeats in Protein Sequences.
multiple sequence alignment
profile analysis
protein sequence analysis
proteome analysis
tandem repeats
Journal
Journal of molecular biology
ISSN: 1089-8638
Titre abrégé: J Mol Biol
Pays: Netherlands
ID NLM: 2985088R
Informations de publication
Date de publication:
28 05 2021
28 05 2021
Historique:
received:
29
09
2020
revised:
01
02
2021
accepted:
21
02
2021
entrez:
11
5
2021
pubmed:
12
5
2021
medline:
25
8
2021
Statut:
ppublish
Résumé
Ensembles of tandem repeats (TRs) in protein sequences expand rapidly to form domains well suited for interactions with proteins. For this reason, they are relatively frequent. Some TRs have known structures and therefore it is advantageous to predict their presence in a protein sequence. However, since most TRs diverge quickly, their detection by classical sequence comparison algorithms is not very accurate. Previously, we developed a method and a web server that used curated profiles and thresholds for the detection of 11 common TRs. Here we present a new web server (REP2) that allows the analysis of TRs in both individual and aligned sequences. We provide currently precomputed analyses for a selection of 78 UniProt reference proteomes. We illustrate how these data can be used to study the evolution of TRs using comparative genomics. REP2 can be accessed at http://cbdm-01.zdv.uni-mainz.de/~munoz/rep/.
Identifiants
pubmed: 33972020
pii: S0022-2836(21)00089-9
doi: 10.1016/j.jmb.2021.166895
pii:
doi:
Substances chimiques
Proteins
0
Proteome
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
166895Informations de copyright
Copyright © 2021 The Authors. Published by Elsevier Ltd.. All rights reserved.
Déclaration de conflit d'intérêts
Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.