• peaks2utr: a robust Python too...

Treffer: peaks2utr: a robust Python tool for the annotation of 3' UTRs.

Title:
peaks2utr: a robust Python tool for the annotation of 3' UTRs.
Authors:
Haese-Hill W; School of Infection & Immunity, MVLS, University of Glasgow, Glasgow G12 8TA, United Kingdom., Crouch K; School of Infection & Immunity, MVLS, University of Glasgow, Glasgow G12 8TA, United Kingdom., Otto TD; School of Infection & Immunity, MVLS, University of Glasgow, Glasgow G12 8TA, United Kingdom.
Source:
Bioinformatics (Oxford, England) [Bioinformatics] 2023 Mar 01; Vol. 39 (3).
Publication Type:
Journal Article; Research Support, Non-U.S. Gov't
Language:
English
Journal Info:
Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print Cited Medium: Internet ISSN: 1367-4811 (Electronic) Linking ISSN: 13674803 NLM ISO Abbreviation: Bioinformatics Subsets: MEDLINE
Imprint Name(s):
Original Publication: Oxford : Oxford University Press, c1998-
MeSH Terms:
Software* , Gene Expression Profiling*, 3' Untranslated Regions
References:
Front Genet. 2018 Dec 18;9:671. (PMID: 30619487)
Genomics Proteomics Bioinformatics. 2021 Apr;19(2):253-266. (PMID: 33662621)
Cold Spring Harb Perspect Biol. 2019 Oct 1;11(10):. (PMID: 30181377)
BMC Genomics. 2017 Nov 6;18(1):847. (PMID: 29110697)
Nucleic Acids Res. 2016 Jul 8;44(W1):W29-34. (PMID: 27105845)
Genome Biol. 2008;9(9):R137. (PMID: 18798982)
Nat Commun. 2022 Apr 27;13(1):2270. (PMID: 35477703)
Methods. 2015 Jul 15;83:111-7. (PMID: 25899044)
BMC Bioinformatics. 2011 Dec 22;12:491. (PMID: 22192575)
Gigascience. 2021 Feb 16;10(2):. (PMID: 33590861)
Nat Commun. 2021 Sep 6;12(1):5268. (PMID: 34489460)
Grant Information:
104111/Z/14/Z United Kingdom WT_ Wellcome Trust; 218288/Z/19/Z United Kingdom WT_ Wellcome Trust
Substance Nomenclature:
0 (3' Untranslated Regions)
Entry Date(s):
Date Created: 20230303 Date Completed: 20230314 Latest Revision: 20250530
Update Code:
20250530
PubMed Central ID:
PMC10008064
DOI:
10.1093/bioinformatics/btad112
PMID:
36864613
Database:
MEDLINE

Weitere Informationen

Summary: Annotation of nonmodel organisms is an open problem, especially the detection of untranslated regions (UTRs). Correct annotation of UTRs is crucial in transcriptomic analysis to accurately capture the expression of each gene yet is mostly overlooked in annotation pipelines. Here we present peaks2utr, an easy-to-use Python command line tool that uses the UTR enrichment of single-cell technologies, such as 10× Chromium, to accurately annotate 3' UTRs for a given canonical annotation.
Availability and Implementation: peaks2utr is implemented in Python 3 (≥3.8). It is available via PyPI at https://pypi.org/project/peaks2utr and GitHub at https://github.com/haessar/peaks2utr. It is licensed under GNU GPLv3.
(© The Author(s) 2023. Published by Oxford University Press.)