TY  - JOUR
AU  - Zerihun, Mehari B
AU  - Pucci, Fabrizio
AU  - Peter, Emanuel K
AU  - Schug, Alexander
TI  - pydca v1.0: a comprehensive software for direct coupling analysis of RNA and protein sequences
JO  - Bioinformatics
VL  - 36
IS  - 7
SN  - 1460-2059
CY  - Oxford
PB  - Oxford Univ. Press
M1  - FZJ-2020-01786
SP  - 2264 - 2265
PY  - 2020
AB  - 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.
LB  - PUB:(DE-HGF)16
C6  - pmid:31778142
UR  - <Go to ISI:>//WOS:000536489400043
DO  - DOI:10.1093/bioinformatics/btz892
UR  - https://juser.fz-juelich.de/record/875075
ER  -