Important Notice
IMPORTANT NOTICE TO ANNOTATION ENGINE USERS: We are pleased to announce that what was one automated annotation service has now become two. This will allow us to serve twice as many users. What was previously the TIGR/JCVI Annotation Engine service has now branched into two new services: one offered by the J. Craig Venter Institute (JCVI), called "The JCVI Annotation Service", the other offered by the Institute for Genome Sciences (IGS) at the University of Maryland, School of Medicine called "The IGS Annotation Engine". The managers of both services are in active collaboration with one another. We encourage you to explore the web sites of the two services to learn more about the two great choices now available.
What is it?
The IGS Annotation Engine is a FREE resource for genomics researchers and educators bringing advanced bioinformatics tools to the lab bench and the classroom.
Annotation Workshop
A short course on the methods and tools used in prokaryotic annotation is now available.
- Sept. 9 - 10
- Nov. 5 - 6
Funding Source
We gratefully thank the National Institute of General Medical Sciences for funding this project.
Introduction
Fast and inexpensive sequencing technology has made it possible for virtually every university department to acquire the capacity to sequence genomes of their choice in-house or at minimal cost. In order to utilize this data we need robust annotation pipelines, tools for the analysis and evaluation of the data, and researchers trained to make sense of the results. However, it is quite costly and time consuming to acquire the considerable infrastructure and expertise needed to create annotation pipelines and would be wastefully redundant for individual researchers to recreate these systems over and over. In addition, to ensure that both current and future genomics scientists have the skills needed to correctly make, use, and interpret this data we must provide quality educational resources that provide real-world annotation experience. To meet these needs, the Institute for Genome Sciences (IGS) offers the FREE IGS Annotation Engine service. The IGS Annotation Engine provides 2 services: FREE automated annotation and tools for prokaryotic DNA sequence to researchers who have sequence but not the infrastructure for its analysis; and a resource for course modules and exercises that provide hands-on training in real-world annotation situations.
The service for Researchers: For those researchers who have a prokaryotic genome sequence (it does NOT need to be complete) but who lack the considerable infrastructure and 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, with the data delivered to the researcher in a MySQL database, and 2) the manual annotation tool Manatee. The pipeline in use at IGS is an extension of the one initially developed at The Institute for Genomic Research (TIGR), now JCVI. It is now publicly available within the Ergatis bioinformatics pipeline management package.
With funding from the National Institute of General Medical Sciences, we are working to significantly expand the tools and services provided by the pipeline. In response to user feedback, we are working on improvements that will add several user-requested features and increase interoperability of the system with other tools. Click here for an outline of the current IGS Annotation Engine pipeline. Click here for more information about Manatee. It is important to note that the two components of the Annotation Engine need not always be used together. We have some users who do not intend to perform manual annotation of their data, and they use Component 1 of the service only. Others may wish do manual annotation but instead of using Manatee they may wish to use other manual annotation tools with data from Component 1.
The service for Educators: An important area of focus for the IGS Annotation Engine is the education of future genomics researchers. The IGS Annotation Engine is a valuable tool for the classroom setting. It provides students with an opportunity to do hands-on, real-world annotation while at the same time gaining in-depth understanding of the elements of the annotation process. We are developing course modules in collaboration with researchers/educators at several universities and colleges. We welcome other such collaborations and plan to create a repository of educational resources for general use. If you would like to explore the possibility of using the Annotation Engine in your classroom, please send us an e-mail.
How to submit a genome to the Annotation Engine
Submitting a genome is easy! Simply send us your prokaryotic genome sequence in fasta format. If the genome is in more than one piece (contigs) we will link them together into a 'pseudomolecule' for the purpose of annotation. A spacer sequence (NNNNNCACACACTTAATTAATTAAGTGTGTGNNNNN) that introduces translational stops in all 6 frames is placed between the contigs. If your genome consists of more than one molecule, they are submitted as separate fasta files.
If you have a genome to submit, please contact us for more information.
How to reference use of the IGS Annotation Engine in your publication
We ask that anyone using the IGS Annotation Engine for their work include that information in the Materials and Methods section and to acknowledge us in the Acknowledgements section. Thank You.