dAPE: a web server to detect homorepeats and follow their evolution

Abstract Summary Homorepeats are low complexity regions consisting of repetitions of a single amino acid residue. There is no current consensus on the minimum number of residues needed to define a functional homorepeat, nor even if mismatches are allowed. Here we present dAPE, a web server that helps following the evolution of homorepeats based on orthology information, using a sensitive but tunable cutoff to help in the identification of emerging homorepeats. Availability and Implementation dAPE can be accessed from http://cbdm-01.zdv.uni-mainz.de/∼munoz/polyx. Supplementary information Supplementary data are available at Bioinformatics online.

[1]  Michail Yu. Lobanov,et al.  HRaP: database of occurrence of HomoRepeats and patterns in proteomes , 2013, Nucleic Acids Res..

[2]  L. Mularoni,et al.  Genome-Wide Analysis of Histidine Repeats Reveals Their Role in the Localization of Human Proteins to the Nuclear Speckles Compartment , 2009, PLoS genetics.

[3]  M. Y. Lobanov,et al.  Non-random distribution of homo-repeats: links with biological functions and human diseases , 2016, Scientific Reports.

[4]  R. Guigó,et al.  Comparative analysis of amino acid repeats in rodents and humans. , 2004, Genome research.

[5]  O. Galzitskaya,et al.  Occurrence of disordered patterns and homorepeats in eukaryotic and bacterial proteomes. , 2012, Molecular bioSystems.

[6]  Miguel A. Andrade-Navarro,et al.  FastaHerder2: Four Ways to Research Protein Function and Evolution with Clustering and Clustered Databases , 2016, J. Comput. Biol..

[7]  D. Higgins,et al.  Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega , 2011, Molecular systems biology.

[8]  Andrey V Kajava,et al.  Protein homorepeats sequences, structures, evolution, and functions. , 2010, Advances in Protein Chemistry and Structural Biology.

[9]  Ronald Wetzel,et al.  Oligoproline effects on polyglutamine conformation and aggregation. , 2006, Journal of molecular biology.

[10]  J. Whisstock,et al.  Functional insights from the distribution and role of homopeptide repeat-containing proteins. , 2005, Genome research.

[11]  Martin H. Schaefer,et al.  Evolution and function of CAG/polyglutamine repeats in protein–protein interaction networks , 2012, Nucleic acids research.

[12]  Daniel E. Goldberg,et al.  Asparagine Repeats in Plasmodium falciparum Proteins: Good for Nothing? , 2013, PLoS pathogens.