ReGSP

ReGSP performs homology-based gene searching and visualization using multiple reference sequences to support gene and transcript prediction in newly sequenced genomes.

Key Features:

• Multiple Reference Sequence Support: Accepts multiple reference sequences for homology searches to expand the scope of gene identification across query genomes.
• User-Customizable Searches: Allows customization of search parameters to tailor homology searches and result grouping.
• cPlot Integration: Produces nucleotide dot plots (cPlot) that visualize sequence similarity between query and reference sequences.

Scientific Applications:

• Gene and Transcript Prediction: Supports homology-based identification and annotation of genes and transcripts in newly sequenced genomes using multiple references.
• Organelle Genome Analysis: Facilitates nuanced analysis of organelle genomes and other complex genetic structures by comparing queries to multiple reference sequences.

Methodology:

Performs homology-based searches using BLAST; groups BLAST results by user-defined parameters; generates nucleotide dot plots via cPlot to visualize sequence similarities.