Contigs and Sequences

A contig is a contiguous sequence of DNA. A contig is conceptually similar to a chromosome; however, in the Sprout Database, a single chromosome may be represented as multiple contigs because we do not yet know how they fit together.

Most bacteria and archaea have a single looped chromosome. If a genome for one of these types of organisms has many contigs, it is generally an indication that the genome is not complete: the theory being that when more data is available we will be able to stitch all the pieces into a single contig. Most eukaryotes have one or more linear chromosomes capped at the end by telomeres. In this case, we expect the number of contigs to eventually drop to the number of chromosomes.

Each contig in the Sprout Database has a unique ID which consists of the genome ID followed by a string of letters and numbers assigned when the genome was originally sequenced.

If you know the contig ID, you can type it into the NMPDR Banner search box to see that contig on the Genome Viewer Browser Page? . The top of the browser page contains a small form for selecting a contig and a location. A visual display of the genes in the selected region is shown next to the form. The genes are also listed in an Interactive Table in the lower section of the same page.

The number of contigs for each genome in the database is displayed as part of the standard Genome Control. Use the form below to select a genome and bring it up in the Genome Viewer Browser Page? . From there, you can select any contig and view its information.

Type to narrow selection (help)

Type to narrow selection (help)

Topic revision: r1 - 04 Jan 2009 - 09:42:54 - Bruce Parrello

Notice to NMPDR Users - The NMPDR BRC contract has ended and bacterial data from NMPDR has been transferred to PATRIC (http://www.patricbrc.org), a new consolidated BRC for all NIAID category A-C priority pathogenic bacteria. NMPDR was a collaboration among researchers from the Computation Institute of the University of Chicago, the Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the National Center for Supercomputing Applications (NCSA) at the University of Illinois. NMPDR is funded by the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under Contract HHSN266200400042C. Banner images are copyright © Dennis Kunkel.