Gene Prediction & Annotation Pipelines — Hands-on

Gain expertise in gene prediction and functional annotation pipelines with practical ORF calling, evidence integration, and publish-ready reporting.

Gene Prediction & Annotation Pipelines

Session Index

Session 1

Fee: Rs 6300

ORF Calling & Evidence

Ab initio ORF detection and parameters

Prodigal EMBOSS getorf Glimmer

Evidence integration from protein/nucleotide homology

BLAST+ DIAMOND MMseqs2

Strand, frame, start codon choice & CDS boundary checks

Frame checks Start/Stop rules

Session 2

Fee: Rs 8400

Domains & HMM Annotation

Protein domain mapping and HMM profile searches

InterProScan HMMER3 Pfam

Signal peptides, transmembranes & localization hints

SignalP TMHMM TargetP

Annotation evidence codes and confidence scoring

ECO GO terms

Session 3

Fee: Rs 11200

Functional Mapping & QC

Annotation transfer and orthology-based mapping

Prokka eggNOG-mapper UniRef

Parsing and reconciling GFF3/BED features at scale

gffread BCBio.GFF bedtools

Codon usage, frameshift & nonsense mutation checks

EMBOSS cusp CodonW FrameDP

Session 4

Fee: Rs 14000

Mini Capstone: End-to-End Annotation

Design reproducible pipeline: input to annotated GFF3

Theory

Automate ORF→domains→functions with reports

Snakemake Conda/Mamba MultiQC

Deliver final annotation package & summary dashboard

pandas JupyterLab Quarto

PDF

Gene Prediction & Functional Annotation Pipelines Training | ORFs, InterProScan, Prokka, GFF3