Transcriptologs

Transcriptologs predicts orthologous genes between two species by comparing translated mRNA fragments to identify orthology from transcript-level data when protein annotations or proteome validation are incomplete.

Key Features:

• Transcript-based ortholog prediction: Uses translated mRNA fragments instead of relying solely on annotated protein sequences to detect orthologous relationships.
• BLAST alignment extension: Extends BLAST alignments to improve coverage and capture weak or subtle similarities between translated transcripts.
• Bidirectional Best Hit orthology criterion: Assigns orthology using a Bidirectional Best Hit (reciprocal best match) approach from pairwise BLAST searches.

Scientific Applications:

• Gene evolution and phylogenetics: Provides ortholog sets for reconstructing evolutionary histories and identifying conserved genetic elements across species.
• Gene function prediction: Enables inference of gene function in less-studied species by transferring annotations from orthologs in model organisms.
• Benchmarking with plant transcriptomes: Demonstrated improved alignment quality and detection of transcript similarities in a test comparison between Arabidopsis thaliana and Sorghum bicolor versus protein-based analyses.

Methodology:

mRNA fragments are translated to amino acid sequences; BLAST alignments are computed and extended to improve coverage and accuracy; orthologs are defined by applying the Bidirectional Best Hit criterion on reciprocal BLAST searches.