TY - JOUR
T1 - A comparative benchmark of classic DNA motif discovery tools on synthetic data
AU - Castellana, Stefano
AU - Biagini, Tommaso
AU - Parca, Luca
AU - Petrizzelli, Francesco
AU - Bianco, Salvatore Daniele
AU - Vescovi, Angelo Luigi
AU - Carella, Massimo
AU - Mazza, Tommaso
N1 - © The Author(s) 2021. Published by Oxford University Press. All rights reserved. For Permissions, please email: [email protected].
PY - 2021/11/1
Y1 - 2021/11/1
N2 - Hundreds of human proteins were found to establish transient interactions with rather degenerated consensus DNA sequences or motifs. Identifying these motifs and the genomic sites where interactions occur represent one of the most challenging research goals in modern molecular biology and bioinformatics. The last twenty years witnessed an explosion of computational tools designed to perform this task, whose performance has been last compared fifteen years ago. Here, we survey sixteen of them, benchmark their ability to identify known motifs nested in twenty-nine simulated sequence datasets, and finally report their strengths, weaknesses, and complementarity.
AB - Hundreds of human proteins were found to establish transient interactions with rather degenerated consensus DNA sequences or motifs. Identifying these motifs and the genomic sites where interactions occur represent one of the most challenging research goals in modern molecular biology and bioinformatics. The last twenty years witnessed an explosion of computational tools designed to perform this task, whose performance has been last compared fifteen years ago. Here, we survey sixteen of them, benchmark their ability to identify known motifs nested in twenty-nine simulated sequence datasets, and finally report their strengths, weaknesses, and complementarity.
KW - benchmark
KW - computational biology
KW - genomics
KW - motif
KW - sequence pattern
UR - http://www.scopus.com/inward/record.url?scp=85121951421&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85121951421&partnerID=8YFLogxK
U2 - 10.1093/bib/bbab303
DO - 10.1093/bib/bbab303
M3 - Article
C2 - 34351399
AN - SCOPUS:85121951421
SN - 1477-4054
VL - 22
JO - Briefings in bioinformatics
JF - Briefings in bioinformatics
IS - 6
M1 - bbab303
ER -