• Parsing GTF and FASTA files us...

Treffer: Parsing GTF and FASTA files using the eccLib Library.

Title:
Parsing GTF and FASTA files using the eccLib Library.
Authors:
Chady T; Department of Mathematical Statistics and Data Analysis, Faculty of Mathematics and Computer Science, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 4, Poznań, 61-614, Poland., Filutowska ZK; Department of Gene Expression, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, Poznań, Wielkopolska, 61-614, Poland.
Source:
Bioinformatics (Oxford, England) [Bioinformatics] 2025 Oct 02; Vol. 41 (10).
Publication Type:
Journal Article
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:
Genomics*/methods , Software*, Algorithms ; Programming Languages
References:
Gigascience. 2021 Feb 16;10(2):. (PMID: 33594436)
Nucleic Acids Res. 2025 Jan 6;53(D1):D948-D957. (PMID: 39656687)
Brief Bioinform. 2021 Jul 20;22(4):. (PMID: 33341884)
Nature. 2020 Sep;585(7825):357-362. (PMID: 32939066)
Bioinformatics. 2020 Feb 1;36(3):918-919. (PMID: 31373614)
J Biotechnol. 2017 Nov 10;261:157-168. (PMID: 28888961)
Nucleic Acids Res. 1985 May 10;13(9):3021-30. (PMID: 2582368)
Grant Information:
0054/DIA/2014/43 Polish Ministry of Education and Science
Entry Date(s):
Date Created: 20251007 Date Completed: 20251024 Latest Revision: 20251027
Update Code:
20260130
PubMed Central ID:
PMC12552103
DOI:
10.1093/bioinformatics/btaf558
PMID:
41056409
Database:
MEDLINE

Weitere Informationen

Summary: Leveraging the Python/C API, eccLib was developed as a high-performance library designed for parsing genomic files and analysing genomic contexts. To the best of the authors' knowledge, it is the fastest Python-based solution available. With eccLib, users can efficiently parse GTF/GFFv3 and FASTA files and utilize the provided methods for additional analysis.
Availability and Implementation: This library is implemented in C and distributed under the GPL-3.0 licence. It is compatible with any system that has the Python interpreter (CPython) installed. The use of C enables numerous optimizations at both the implementation and algorithmic levels, which are either unachievable or impractical in Python.
(© The Author(s) 2025. Published by Oxford University Press.)