Journal Article

FZJ-2020-01786

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png pydca v1.0: a comprehensive software for direct coupling analysis of RNA and protein sequences

Zerihun, M. B.FZJ* ; Pucci, F.FZJ* ; Peter, E. K.FZJ* ; Schug, A. (Corresponding author)FZJ*

2020
Oxford Univ. Press Oxford

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Please use a persistent id in citations: http://hdl.handle.net/2128/24703  doi:10.1093/bioinformatics/btz892

Abstract: The ongoing advances in sequencing technologies have provided a massive increase inthe availability of sequence data. This made it possible to study the patterns of correlated substitutionbetween residues in families of homologous proteins or RNAs and to retrieve structural and stabilityinformation. Direct coupling Analysis (DCA) infers coevolutionary couplings between pairs of residuesindicating their spatial proximity, making such information a valuable input for subsequent structureprediction. Here we presentpydca, a standalone Python-based software package for the DCA ofprotein- and RNA-homologous families. It is based on two popular inverse statistical approaches,namely, the mean-field and the pseudo-likelihood maximization and is equipped with a series offunctionalities that range from multiple sequence alignment trimming to contact map visualization.Thanks to its efficient implementation, features and user-friendly command line interface,pydcaisa modular and easy-to-use tool that can be used by researchers with a wide range of backgrounds.

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Contributing Institute(s):

1. Jülich Supercomputing Center (JSC)
2. John von Neumann - Institut für Computing (NIC)

Research Program(s):

1. 511 - Computational Science and Mathematical Methods (POF3-511) (POF3-511)
2. PhD no Grant - Doktorand ohne besondere Förderung (PHD-NO-GRANT-20170405) (PHD-NO-GRANT-20170405)

Appears in the scientific report 2020

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Database coverage:
; ; BIOSIS Previews ; Clarivate Analytics Master Journal List ; Current Contents - Life Sciences ; Ebsco Academic Search ; IF >= 5 ; JCR ; NCBI Molecular Biology Database ; Nationallizenz ; PubMed Central ; SCOPUS ; Science Citation Index ; Science Citation Index Expanded ; Web of Science Core Collection

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