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)
"""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."""
 * Augustus HTML
 * GeneZilla
 * Conrad java standalone

Korf, Ian. “Gene finding in novel genomes.” BMC Bioinformatics 5, no. 1 (2004): 59.
 * SNAP from Ian Korf: ik1@sanger.ac.uk

Prokaryots

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