NMPDR has released new genome annotations for each of the focus organisms in modified GFF3 format. GFF3, described at the Sequence Ontology website, is a flat file format for describing genomic features. The formatted GFF3 files accessible below contain rows of records, each with nine tab-delimited fields: seqid, source, type, start, end, score, strand, phase, and attributes. The score and phase fields are not in use, so in each row, those fields contain the period (.) character. Each row describes a feature, which is a region on the DNA located between start and end nucleotide coordinates. To describe a protein-encoding gene, two rows are used to record two features at the same location: gene and CDS. FASTA formatted nucleotide and amino acid sequences follow the tab-delimited table of feature annotations.

Topic revision: r4 - 16 Jan 2009 - 20:09:34 - TWiki Guest
Main.NmpdrDownloads moved from Main.NMPDRDownloads on 22 Dec 2008 - 22:29 by TWiki Guest - put it back
Notice to NMPDR Users - The NMPDR BRC contract has ended and bacterial data from NMPDR has been transferred to PATRIC (, 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.