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Tytuł pozycji:

BiasAway: command-line and web server to generate nucleotide composition-matched DNA background sequences.

Tytuł:
BiasAway: command-line and web server to generate nucleotide composition-matched DNA background sequences.
Autorzy:
Khan A; Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0349 Oslo, Norway.; Stanford University School of Medicine, Stanford Cancer Institute, Stanford, CA 94304, USA.
Riudavets Puig R; Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0349 Oslo, Norway.
Boddie P; Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0349 Oslo, Norway.
Mathelier A; Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0349 Oslo, Norway.; Department of Medical Genetics, Oslo University Hospital, 0424 Oslo, Norway.
Źródło:
Bioinformatics (Oxford, England) [Bioinformatics] 2021 Jul 12; Vol. 37 (11), pp. 1607-1609.
Typ publikacji:
Journal Article; Research Support, Non-U.S. Gov't
Język:
English
Imprint Name(s):
Original Publication: Oxford : Oxford University Press, c1998-
MeSH Terms:
Genomics*
Software*
DNA/genetics ; Genome ; Nucleotides
References:
Genome Res. 2000 Dec;10(12):1986-95. (PMID: 11116093)
Front Genet. 2016 Feb 23;7:24. (PMID: 26941778)
PLoS One. 2012;7(11):e47836. (PMID: 23144830)
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Cell. 2014 Sep 11;158(6):1431-1443. (PMID: 25215497)
Nature. 2015 Feb 19;518(7539):317-30. (PMID: 25693563)
BMC Bioinformatics. 2008 Apr 11;9:192. (PMID: 18405375)
Nat Methods. 2018 Jul;15(7):475-476. (PMID: 29967506)
Nucleic Acids Res. 2018 Jul 2;46(W1):W209-W214. (PMID: 29722874)
Cell. 2018 Oct 4;175(2):598-599. (PMID: 30290144)
Nat Rev Genet. 2011 Jan;12(1):32-42. (PMID: 21102527)
BMC Genomics. 2014 Jun 13;15:472. (PMID: 24927817)
Cell Syst. 2017 Dec 27;5(6):654. (PMID: 29284131)
Eur J Biochem. 1970 Aug;15(2):203-8. (PMID: 5502660)
Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W119-27. (PMID: 18495751)
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Grant Information:
187615 Norwegian Research Council; Helse Sør-Øst and the University of Oslo through the Centre for Molecular Medicine Norway; 288404 Norwegian Research Council; 197884 Norwegian Cancer Society
Substance Nomenclature:
0 (Nucleotides)
9007-49-2 (DNA)
Entry Date(s):
Date Created: 20201102 Date Completed: 20210715 Latest Revision: 20230519
Update Code:
20240105
PubMed Central ID:
PMC8275979
DOI:
10.1093/bioinformatics/btaa928
PMID:
33135764
Czasopismo naukowe
Motivation: Accurate motif enrichment analyses depend on the choice of background DNA sequences used, which should ideally match the sequence composition of the foreground sequences. It is important to avoid false positive enrichment due to sequence biases in the genome, such as GC-bias. Therefore, relying on an appropriate set of background sequences is crucial for enrichment analysis.
Results: We developed BiasAway, a command line tool and its dedicated easy-to-use web server to generate synthetic sequences matching any k-mer nucleotide composition or select genomic DNA sequences matching the mononucleotide composition of the foreground sequences through four different models. For genomic sequences, we provide precomputed partitions of genomes from nine species with five different bin sizes to generate appropriate genomic background sequences.
Availability and Implementation: BiasAway source code is freely available from Bitbucket (https://bitbucket.org/CBGR/biasaway) and can be easily installed using bioconda or pip. The web server is available at https://biasaway.uio.no and a detailed documentation is available at https://biasaway.readthedocs.io.
Supplementary Information: Supplementary data are available at Bioinformatics online.
(© The Author(s) 2020. Published by Oxford University Press.)

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