QPARSE: searching for long-looped or multimeric G-quadruplexes potentially distinctive and druggable.
Bioinformatics
; 36(2): 393-399, 2020 01 15.
Article
em En
| MEDLINE
| ID: mdl-31328780
ABSTRACT
MOTIVATION G-quadruplexes (G4s) are non-canonical nucleic acid conformations that are widespread in all kingdoms of life and are emerging as important regulators both in RNA and DNA. Recently, two new higher-order architectures have been reported adjacent interacting G4s and G4s with stable long loops forming stem-loop structures. As there are no specialized tools to identify these conformations, we developed QPARSE. RESULTS:
QPARSE can exhaustively search for degenerate potential quadruplex-forming sequences (PQSs) containing bulges and/or mismatches at genomic level, as well as either multimeric or long-looped PQS (MPQS and LLPQS, respectively). While its assessment versus known reference datasets is comparable with the state-of-the-art, what is more interesting is its performance in the identification of MPQS and LLPQS that present algorithms are not designed to search for. We report a comprehensive analysis of MPQS in human gene promoters and the analysis of LLPQS on three experimentally validated case studies from HIV-1, BCL2 and hTERT. AVAILABILITY AND IMPLEMENTATION QPARSE is freely accessible on the web at http//www.medcomp.medicina.unipd.it/qparse/index or downloadable from github as a python 2.7 program https//github.com/B3rse/qparse. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Texto completo:
1
Bases de dados:
MEDLINE
Assunto principal:
Quadruplex G
Limite:
Humans
Idioma:
En
Revista:
Bioinformatics
Assunto da revista:
INFORMATICA MEDICA
Ano de publicação:
2020
Tipo de documento:
Article
País de afiliação:
Itália