SeqTailor

SeqTailor extracts DNA and protein sequences from Variant Call Format (VCF) files to provide sequence context for downstream analyses of next-generation sequencing (NGS) variants, including splicing prediction, sequence alignment, phylogenetic analysis, and protein structure prediction.

Key Features:

• Rapid sequence extraction: Extracts DNA sequences surrounding genomic variants from VCF files with configurable window sizes, annotates nearest splice sites, and considers neighboring variants within the specified window.
• Protein sequence encoding: Derives protein sequences encoded by variant-containing DNA sequences and integrates SnpEff for variant effect annotation.
• Customizable parameters: Allows specification of window sizes for both DNA and protein sequence extraction and related annotation parameters.
• Multi-species support: Supports human (GRCh37 and GRCh38), chimpanzee, mouse, rat, cow, chicken, lizard, zebrafish, fruitfly, Arabidopsis, and rice.

Scientific Applications:

• Splicing prediction: Provides DNA sequence contexts and splice-site annotation to inform prediction of variant effects on splicing.
• Sequence alignment: Supplies variant-centered DNA or protein sequences for accurate alignment and comparative analyses.
• Phylogenetic analysis: Delivers sequences across supported species to assist in reconstructing evolutionary relationships.
• Structure prediction: Provides protein sequences reflecting variant-induced changes to enable protein structure modeling and analysis.

Methodology:

SeqTailor processes VCF files to extract DNA and protein sequences with user-specified window sizes, considers neighboring variants within windows, annotates nearest splice sites and variant effects, and integrates SnpEff for effect annotation.