PT  - JOURNAL ARTICLE
AU  - Mehari B. Zerihun
AU  - Fabrizio Pucci
AU  - Emanuel Karl Peter
AU  - Alexander Schug
TI  - pydca v1.0: a comprehensive software for Direct Coupling Analysis of RNA and Protein Sequences
AID  - 10.1101/805523
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 805523
4099  - http://biorxiv.org/content/early/2019/10/15/805523.short
4100  - http://biorxiv.org/content/early/2019/10/15/805523.full
AB  - The ongoing advances in sequencing technologies have provided a massive increase in the availability of sequence data. This made it possible to study the patterns of correlated substitution between residues in families of homologous proteins or RNAs and to retrieve structural and stability information. Direct coupling Analysis (DCA) infers coevolutionary couplings between pairs of residues indicating their spatial proximity, making such information a valuable input for subsequent structure prediction. Here we present pydca, a standalone Python-based software package for the DCA of protein- 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 of functionalities that range from multiple sequence alignment trimming to contact map visualization. Thanks to its efficient implementation, features and user-friendly command line interface, pydca is a modular and easy-to-use tool that can be used by researchers with a wide range of backgrounds.Availability https://github.com/KIT-MBS/pydca