PHi-C2: interpreting Hi-C data as the dynamic 3D genome state.
Journal
Bioinformatics (Oxford, England)
ISSN: 1367-4811
Titre abrégé: Bioinformatics
Pays: England
ID NLM: 9808944
Informations de publication
Date de publication:
31 10 2022
31 10 2022
Historique:
received:
07
05
2022
revised:
14
08
2022
pubmed:
11
9
2022
medline:
3
11
2022
entrez:
10
9
2022
Statut:
ppublish
Résumé
High-throughput chromosome conformation capture (Hi-C) is a widely used assay for studying the three-dimensional (3D) genome organization across the whole genome. Here, we present PHi-C2, a Python package supported by mathematical and biophysical polymer modeling that converts input Hi-C matrix data into the polymer model's dynamics, structural conformations and rheological features. The updated optimization algorithm for regenerating a highly similar Hi-C matrix provides a fast and accurate optimal solution compared to the previous version by eliminating the factors underlying the inefficiency of the optimization algorithm in the iterative optimization process. In addition, we have enabled a Google Colab workflow to run the algorithm, wherein users can easily change the parameters and check the results in the notebook. Overall, PHi-C2 represents a valuable tool for mining the dynamic 3D genome state embedded in Hi-C data. PHi-C2 as the phic Python package is freely available under the GPL license and can be installed from the Python package index. The source code is available from GitHub at https://github.com/soyashinkai/PHi-C2. Moreover, users do not have to prepare a Python environment because PHi-C2 can run on Google Colab (https://bit.ly/3rlptGI). Supplementary data are available at Bioinformatics online.
Identifiants
pubmed: 36087002
pii: 6695219
doi: 10.1093/bioinformatics/btac613
pmc: PMC9620818
doi:
Substances chimiques
Polymers
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
4984-4986Informations de copyright
© The Author(s) 2022. Published by Oxford University Press.
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