Wikiomics:Genome annotation

Genome annotation process of finding functional (genes, regulatory elements, ncRNAs) and non-functional features (repeats) in the genomic sequence.

Gene finding

Comparative

Side issue: accurate cross-species genomic alignments

• GRAPe GRAPe is a tool for computing genome re-alignment using marginalized posterior decoding.

Eukariota

• SLAM HTML
• TWAIN HTML
• PROJECTOR @Sanger
• DOUBLESCAN
• N-SCAN PDF
• AAT
• EVOGENE
• SGP2

• yrGATE HTML Plant comparative genomics

Prokariota

• GLIMMER

de novo

• Jigsaw meta-program designed to use the output from gene finders, splice site prediction programs and sequence alignments to predict gene models.

Eukariota, genomic level)

• Augustus HTML
• GeneZilla
• Conrad java standalone

"""The Conrad gene caller is tool for predicting gene structures in DNA based on the DNA sequence and other available evidence. The gene caller uses semi-Markov Conditional Random Fields. The Conrad CRF engineis a general purpose CRF engine used by the gene caller to provide the structure and algorithms for gene calling."""

• SNAP from Ian Korf: ik1@sanger.ac.uk

Korf, Ian. “Gene finding in novel genomes.” BMC Bioinformatics 5, no. 1 (2004): 59.

Prokaryots

• Bremen pipeline described in PNAS
• JCOAST "java based program for comparative genomics working on top of GenDB v2.2 projects".