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Glossary of Useful Terms

• Alias An alias is a gene identifier from an outside organization or database. Inside the NMPDR's data structures, the FigId is used for each gene. Each gene also has a list ...
• Assertion An assertion is a statement about the purpose of a particular feature in a genome . The most common type of assertion is the assignment of a FunctionalRole ...
• BidirectionalBestHit BBH example: the black arrows represent best hits. The best hit of a particular gene to a target genome is the gene in that genome that represents a best ...
• CoreOrganisms NMPDR is a Bioinformatics Resource Center. Each center specializes in certain pathogens. In NMPDR, we call these the core genomes or NMPDR genomes . The genomes ...
• FastaFormat FASTA format is a standard format for encoding DNA or protein sequences. A FASTA file generally contains one or more sequences in FASTA format. A single sequence ...
• Feature Features and Genes A feature is anything that can be mapped onto a strand of DNA, and is defined by its start and stop location. Feature is a catch all, general ...
• FigFam FigFams are sets of ProteinSequences that are similar along their full length. Proteins are thought of as implementing one or more abstract FunctionalRoles. All of ...
• FigId Every gene in the NMPDR database has a unique FigId. It has four parts, as shown in the diagram below. /FigID.png The prefix identifies the fact that this ...
• FunctionalRole The functional role of a feature is the task it performs in the host organism. The role is stored in the NMPDR database as a descriptive phrase. Some functional ...
• Genome Screen shot from the GenomeViewer showing a section of genome A genome is a related collection of DNA. In most cases, a genome represents the DNA for a single sequenced ...
• Homologs Two features are said to be similar or homologous if they share a nearly identical DNA sequence. Two similar features are called homologs , and the set of one ...
• Motif A protein motif is a small section of a protein that has a known function, is folded independently of the rest if the protein, or functions as a docking site. The ...
• ProteinEncodingGene Protein encoding gene (PEG), protein coding sequence (CDS), and open reading frame (ORF) are synonymous terms. Protein encoding genes are commmonly described as structural ...
• Subsystem Subsystem diagram for , an example of a subsystem based on a metabolic pathway. Subsystems are a generalization of the concept of pathways, and they have two components ...