All identified hits were confirmed using the gene finding tool Glimmer and the gene annotation tool Manatee from The Institute For Genomic Research TIGRR) [41].
De novo ORF predictions were also made using three prokaryotic gene finding tools: Glimmer [99], Prodigal (http://compbio.ornl.gov/prodigal/), and Metagene [100].
For the prediction of coding sequences (CDSs), we first combined the tools Glimmer and Critica [ 29, 30] in Reganor [ 31] and subsequently integrated Reganor into GenDB.
In order to optimize results and allow for easy manual curation, further intrinsic, extrinsic and combined methods were applied by means of the Reganor software [ 100, 101] which utilizes the popular gene prediction tools Glimmer [ 102] and CRITICA [ 103].
After sequencing a new genome their existence is predicted by annotation tools, e.g., GLIMMER [ 20, 21] or GeneMarkS [ 22].
For this stage of the course, students paired up in teams of two and worked on annotating specific sections of the sequenced genome using Genemark (http://exon.gatech.edu) and Glimmer (www.cbcb.umd.edu/software/glimmer) software tools.
Annotation of all open reading frames (ORFs) was carried out using Glimmer, GeneMark, JGI annotation tools and GAMOLA [ 30], before manual checking of all predicted genes.
The mitochondrial sequences were annotated with Glimmer 3.0 and BLAST tools, and tRNA genes and their secondary structures were identified according to tRNA scan-SE [ 52].
Here we draw attention to a large number of likely genes missing from annotations using common tools such as Glimmer and BLAST.
Protein-coding genes were annotated using the online ORF Finder tool [ 52]; the software Glimmer 3.02 [ 53] under iterated pipeline for assessing ORF features was used to confirm results; homology search was carried out with BLAST ([ 54, 55]; and reference therein]).
