GFFStrandLoc: Strand-Wise Gene and Protein Extraction from GFF3 Files

Facilitates the extraction and organization of strand-specific genomic features from GFF3 files. In many species and variants, high quality genome annotations are not always available, necessitating de novo annotation using tools such as AUGUSTUS (Stanke et al., 2006; <doi:10.1093/nar/gkl200>). However, downstream processing of such annotations to obtain structured information, such as strand-wise gene locations, transcript regions, and associated protein identifiers—can be computationally intensive and complex. 'GFFStrandLoc' provides a streamlined framework to parse GFF3 files and generate structured outputs containing strand-wise and region-wise genomic coordinates for each transcript, along with their associated protein information. Additionally, it enables users to define custom promoter lengths and extract corresponding promoter region coordinates for genes in a strand-aware manner. By simplifying post-annotation processing, it enhances the usability of de novo annotated genomic datasets for downstream analysis and interpretation.

Version:	0.1.0
Published:	2026-04-15
DOI:	10.32614/CRAN.package.GFFStrandLoc (may not be active yet)
Author:	Subham Ghosh [aut, cre], Monendra Grover [aut], Dipro Sinha [aut], Dwijesh Mishra [aut], Sneha Murmu [aut], Sayanti Guha Majumdar [aut], UB Angadi [aut], Md Yeasin [aut]
Maintainer:	Subham Ghosh <search4aghosh at gmail.com>
License:	GPL-3
NeedsCompilation:	no
CRAN checks:	GFFStrandLoc results

Documentation:

Reference manual:

GFFStrandLoc.html , GFFStrandLoc.pdf

Downloads:

Package source:	GFFStrandLoc_0.1.0.tar.gz
Windows binaries:	r-devel: not available, r-release: GFFStrandLoc_0.1.0.zip, r-oldrel: not available
macOS binaries:	r-release (arm64): not available, r-oldrel (arm64): not available, r-release (x86_64): GFFStrandLoc_0.1.0.tgz, r-oldrel (x86_64): not available

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