Segtor: rapid annotation of genomic coordinates and single nucleotide variations using segment trees

Area of Science:

• Genomics
• Bioinformatics
• Computational Biology

Background:

• Next-generation sequencing generates massive datasets requiring efficient annotation.
• Determining the positional relationship of genomic variations to genes is crucial for understanding their functional impact.
• Existing annotation methods may struggle with the scale of modern genomic data.

Purpose of the Study:

• To introduce Segtor, a novel computational tool for annotating large-scale genomic datasets.
• To provide an efficient method for determining the relative positions of genomic features like SNVs, indels, and translocations with respect to genes.
• To offer annotation statistics for visualizing the distribution of genomic coordinates within gene structures.

Main Methods:

• Segtor utilizes segment trees built from genomic feature coordinates, avoiding traditional database management systems.
• The software processes large sets of genomic coordinates, intervals, SNVs, indels, and translocations.
• It is compatible with any species available on the UCSC Genome Browser.

Main Results:

• Segtor enables the annotation of extensive genomic datasets, including millions of individual genomes.
• The tool efficiently determines the position of genomic variations relative to genes and their impact on protein translation.
• Annotation statistics are generated, allowing users to visualize coordinate distribution within gene regions.

Conclusions:

• Segtor is a valuable, open-source tool for researchers needing to annotate large genomic datasets, particularly those with limited programming resources.
• Its segment tree approach offers an efficient alternative to database-dependent methods for genomic annotation.
• The tool facilitates the analysis of genomic variations and their potential effects on gene function across various species.