RefSeq

To create our terminology containing both internal terms and external terms we semiautomatically extract terms from available external resources (e.g., MeSH, EMTREE, UniProt). Then we fit the extracted terms to our data structure and preserve the reference to the source system because sometimes terms are very specific to certain databases. We refer to the terms specific to a database as local terms. These local terms are stored in a dedicated data structure, the Metastore. It must be noted that we refer to accession codes and identifiers used in databases such as UniProt, RefSeq, and GO as local terms (see Tables 31.1 and 31.2). 

BioFocus DPI) collection of chemical series from medchem literature nal chemistry journals RefSeq or ACCESSION... 

RefSeq (Reference Sequences) e CDD (Conserved Domain Database)... 

RefSeq. NCBI. URL http //www.ncbi.nlm.nih.gov/RefSeq/. A comprehensive, integrated, nonredundant set of reference... 

Pruitt, K. D., Tatusova, T and Maglott, D. R. (2005) NCBI Reference Sequence (RefSeq) a curated non-redundant sequence database of genomes, transcripts, and proteins. Nucleic Acid Res. 33, D501-D504. 

When uploading sequence files to generate a comparison, the volume of data to be transferred to the WebACT server can be considerable. If certain sequences in the comparison are present in the EMBL or RefSeq databases, try to use these in preference to uploading them, because this should produce much faster results. 

It is worth remarking that the RefSeq (Reference Sequence) number for a genome generally corresponds to the number on the Accession line of its documentation, and is often referred to as the Accession number. In this chapter, we shall use the term RefSeq number throughout for consistency. 

When conversion is complete the user will receive a message containing the filenames of the Data and Sequence files generated. These are based on the RefSeq number of the genome, and are given the extensions .gda and .seq, respectively. 

The user will be prompted to name the file being generated, and the user will be able to navigate through the filespace to the directory where it will be saved. It is recommended that the file be saved to the same directory as the associated genome files, and that its name should reference the RefSeq numbers of these (see Note 7) and have the extension. gcf (e.g., NC 003112-NC 003116.gcf). 

Clear the contents of the third field and leave it empty. Instead of pasting the large genome. faa file here, upload it from the filespace at the Select input file option using the Browse button. Note the RefSeq number of this file, and the fact that it will subsequently be referred to as the Query genome. 

Choose the second genome from the list on the pull-down menu. The names of the genomes, rather than their RefSeq numbers, are listed on the menu, check to reconcile these, referring to the Genbank website if necessary (see Subheading 2.2.). Make a note of this RefSeq number as that of the Database genome. 

COG information can only be loaded when there is a single genome in the BugView window—if more than one genome has been loaded the menu item will appear dimmed. The reason for this is that the. ptt files contain no internal RefSeq numbers from which the program can determine to which genome they relate. 

If the user is uncertain of the RefSeq numbers of the files loaded into BugView, they can be checked quickly by choosing Genome and Pair Summaries from the View menu. 

A project file can be generated at any time that all five files for a genome comparison (two. gda files, two. seq files, and the. gcf file) are loaded into BugView. Choose New Project File from the file menu, and save to the same directory as the associated data, sequence, and comparison files with a name that references their RefSeq numbers and has the extension. prj (e.g., NC 003112-... 

These have RefSeq numbers NC 003112 and NC 003116, for those who wish to reproduce this example. 

---