• Hypermut 3: identifying specif...

Treffer: Hypermut 3: identifying specific mutational patterns in a defined nucleotide context that allows multistate characters.

Title:
Hypermut 3: identifying specific mutational patterns in a defined nucleotide context that allows multistate characters.
Authors:
Lapp Z; Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, United States., Yoon H; Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, United States., Foley B; Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, United States., Leitner T; Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, United States.
Source:
Bioinformatics advances [Bioinform Adv] 2025 Feb 10; Vol. 5 (1), pp. vbaf025. Date of Electronic Publication: 2025 Feb 10 (Print Publication: 2025).
Publication Type:
Journal Article
Language:
English
Journal Info:
Publisher: Oxford University Press Country of Publication: England NLM ID: 9918282081306676 Publication Model: eCollection Cited Medium: Internet ISSN: 2635-0041 (Electronic) Linking ISSN: 26350041 NLM ISO Abbreviation: Bioinform Adv Subsets: PubMed not MEDLINE
Imprint Name(s):
Original Publication: [Oxford] : Oxford University Press : International Society for Computational Biology, [2021]-
Comments:
Update of: bioRxiv. 2024 Oct 29:2024.10.24.620069. doi: 10.1101/2024.10.24.620069.. (PMID: 39553937)
References:
Nat Struct Mol Biol. 2004 May;11(5):435-42. (PMID: 15098018)
PLoS Pathog. 2012;8(7):e1002800. (PMID: 22807680)
Hepatology. 2005 Mar;41(3):626-33. (PMID: 15726649)
Nat Methods. 2020 Mar;17(3):261-272. (PMID: 32015543)
iScience. 2023 Dec 01;27(1):108601. (PMID: 38188513)
Bioinformatics. 2000 Apr;16(4):400-1. (PMID: 10869039)
J Virol. 1991 Apr;65(4):1779-88. (PMID: 2002543)
Grant Information:
R01 AI087520 United States AI NIAID NIH HHS
Entry Date(s):
Date Created: 20250221 Latest Revision: 20250621
Update Code:
20250621
PubMed Central ID:
PMC11842049
DOI:
10.1093/bioadv/vbaf025
PMID:
39981109
Database:
MEDLINE

Weitere Informationen

Motivation: The detection of APOBEC3F- and APOBEC3G-induced mutations in virus sequences is useful for identifying hypermutated sequences. These sequences are not representative of viral evolution and can therefore alter the results of downstream sequence analyses if included. We previously published the software Hypermut, which detects hypermutation events in sequences relative to a reference. Two versions of this method are available as a webtool. Neither of these methods consider multistate characters or gaps in the sequence alignment.
Results: Here, we present an updated, user-friendly web and command-line version of Hypermut with functionality to handle multistate characters and gaps in the sequence alignment. This tool allows for straightforward integration of hypermutation detection into sequence analysis pipelines. As with the previous tool, while the main purpose is to identify G to A hypermutation events, any mutational pattern and context can be specified.
Availability and Implementation: Hypermut 3 is written in Python 3. It is available as a command-line tool at https://github.com/MolEvolEpid/hypermut3 and as a webtool at https://www.hiv.lanl.gov/content/sequence/HYPERMUT/hypermutv3.html.
(© The Author(s) 2025. Published by Oxford University Press.)

None declared.