Guitar

Guitar maps genome-based coordinates of RNA-related features to standardized transcript-relative coordinates and visualizes their distributions relative to transcript landmarks as an R/Bioconductor package.

Key Features:

• Transcript-relative mapping: Internally extracts standardized RNA coordinates from genome-based coordinates to map features relative to transcript landmarks (transcription start sites, start codons, stop codons, transcription end sites).
• Landmark visualization: Visualizes distributions of RNA-related genomic features with respect to TSS, start codon, stop codon, and TES.
• High-throughput compatibility: Enables analysis of large numbers of RNA-related genomic features within minutes.
• RNA modification analysis: Supports analysis of posttranscriptional RNA modifications including 5-methylcytosine (m(5)C) and N6-methyladenosine.
• Sequencing data support: Works with data derived from high-throughput sequencing techniques such as MeRIP-Seq and RNA BS-Seq.
• R/Bioconductor implementation: Implemented as an open-source R/Bioconductor package for integration with R-based genomic workflows.

Scientific Applications:

• RNA methylation profiling: Analyze distribution and enrichment patterns of modifications such as 5-methylcytosine (m(5)C) and N6-methyladenosine using MeRIP-Seq and RNA BS-Seq data.
• Transcriptome-wide feature distribution: Examine positional enrichment of RNA-related genomic features across transcript landmarks including 5'UTR, coding region, and 3'UTR.
• Biological insight generation: Identify patterns such as reported m(5)C enrichment in 5' untranslated regions (5'UTRs).

Methodology:

Internally extracts standardized transcript-relative coordinates from genome-based coordinates and maps features to transcript landmarks (transcription start sites, start codons, stop codons, transcription end sites).