GeSeq

GeSeq annotates organellar genome sequences, with emphasis on chloroplast genomes, by combining BLAT homology searches, profile HMMs, and de novo tRNA predictors to produce GenBank-format annotations for comparative and phylogenetic analyses.

Key Features:

• Curated chloroplast database: An integrated database of manually curated chloroplast genome sequences is available for reference-based annotation.
• BLAT-based homology searches: Uses BLAT to detect genes and other feature-encoding regions by sequence homology.
• Profile HMM searches: Employs profile HMM searches specifically for protein-coding and rRNA genes.
• De novo tRNA prediction: Incorporates two de novo predictors tailored for identification of tRNA genes.
• Reference selection: Allows selection of organellar genome records from NCBI or use of user-uploaded reference sequences.
• Batch processing: Supports batch processing of multiple organellar genome sequences.
• Comparative annotation: Enables comparison of annotations produced by different methods (BLAT, HMM, de novo) to inform annotation quality.
• GenBank output: Produces annotated genomes in GenBank file format.
• OGDRAW visualization: GenBank outputs can be visualized using OGDRAW.
• Downstream outputs: Provides optional outputs to support comparative genomic studies and phylogenetic research.

Scientific Applications:

• Organellar genome annotation: Annotation of chloroplast and other organellar genomes.
• Gene identification: Identification of protein-coding genes, rRNA genes, and tRNA genes.
• Comparative genomics: Generation of annotated genomes for comparative genomic analyses.
• Phylogenetic research: Provision of data and formats suitable for phylogenetic and evolutionary studies.

Methodology:

BLAT-based homology searches to detect genes and feature-encoding regions; profile HMM searches for protein-coding and rRNA genes; two de novo predictors for tRNA genes; reference selection from NCBI or user-uploaded sequences plus an integrated curated chloroplast genome database; output in GenBank format with optional visualization via OGDRAW.