A short course on the methods and tools used in genomics analysis.
We gratefully thank the National Institute of General Medical Sciences for funding this project.
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.
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 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.
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.
To submit sequence to the Annotation 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.
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.