GTFtools

GTFtools computes and extracts gene model features from ENSEMBL/GENCODE GTF files to support analyses such as intron retention detection, DNA-binding site identification, and splicing strength computation.

Key Features:

• Splice site calculation: Calculates splice sites from GTF gene models.
• Independent intron identification: Identifies independent introns that do not overlap exons of other isoforms.
• TSS-flanking region extraction: Extracts transcription start site (TSS)-flanking regions.
• UTR extraction: Extracts untranslated regions (UTRs) from gene annotations.
• Isoform coordination and length: Computes isoform coordination and individual isoform lengths.
• Gene length calculations: Computes different types of gene lengths.
• Input compatibility: Accepts ENSEMBL and GENCODE GTF files and supports human and non-human gene models such as mouse.
• Implementation: Implemented in Python and operates without reliance on third-party software.
• Comparative functionality: Provides functionalities not present in Bedtools and BioMart, notably calculation of independent introns and splice sites absent from BioMart.

Scientific Applications:

• Intron retention detection: Supplies independent intron and splice site data used to detect intron retention events.
• DNA-binding site identification: Provides TSS-flanking regions and gene feature coordinates useful for DNA-binding site analyses.
• Splicing strength computation: Provides splice site annotations required for splicing strength calculations.
• Gene-centric genomics and transcriptomics: Enables detailed gene model manipulation for genomics, transcriptomics, and molecular biology studies.

Methodology:

Parses ENSEMBL/GENCODE GTF files and computes gene features (splice sites, independent introns, TSS-flanking regions, UTRs, isoform lengths, and gene lengths); implemented in Python.