Analysis - Whole Genome Annotation

Whole Genome Annotation
Automated structural and functional annotation of genomes using the IGS Prokaryotic Annotation Pipeline (PMID:21677861) and the Manatee visualization tool. IGS has developed a comprehensive automated pipeline for use with Bacteria and Archaea. The pipeline predicts protein-coding genes as well as non-coding RNAs. Similarity evidence is collected for predicted proteins with a variety of methods including pairwise alignments, HMM searches, and multiple motif prediction tools. A hierarchical rule-based system is used to assign annotation to each protein based on the highest quality available evidence. Results are loaded into a relational database and can be viewed using the Manatee annotation visualization and curation tool. Results are also available in multiple standard flat file formats.

Submit a sequence
For those researchers who have a prokaryotic genome sequence (draft or complete) but who lack the infrastructure and/or expertise needed for genome annotation, we offer an automatic annotation service. This service consists of two components: 1) the generation of search data and automatic annotation using our prokaryotic annotation pipeline and 2) the manual annotation tool Manatee.

To submit sequence to the Analysis Engine, simply send the sequence in a FASTA formated file. Please don't send zip files as they are blocked by our university mail system but other forms of compression are fine. Please let us know if the genomes are complete or in a draft state. If they are draft genomes there are two options for doing the annotation: 1. on the contigs; 2. on a pseudomolecule (contigs linked together into one long sequence with a spacer between each contig that introduces starts and stops in all 6 frames). We can generate the psueudomolecules for you if you wish us to. Also, if there is a close relative of your strain that has its sequence completed we can use that to order your contigs. If not, we can order the contigs longest to shortest. Please contact us if you are not sure which option (contigs/pseudomolecule) is best for you and we can provide some help in making the decision.

If you have a genome to submit, please contact us for more information.

Educational Resources
View our Tools and Tutorials page for PDFs, demos and links to online web tools.

Training workshops are available on this topic, please click here for more information

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