What tools are in NMPDR?

NMPDR provides tools for comparative analysis of proteins, comparative analysis of genetic and functional contexts of proteins, and comparative analysis of whole genomes. NMPDR provides access to well-known tools written by other institutions, as well as tools developed specifically for NMPDR and SEED.

Tools for comparative analysis of protein sequences include BLAST analyses of orthologs in hundreds of genomes, a protein sequence alignment tool, and several tools for finding amino acid patterns.

Pre-computed BLAST results are available on each protein page via a button that will open a table of bidirectional best hits. For any protein focused on, the best BLAST hit from every subject genome in the database is listed in the table, if the focus protein is the best hit when its genome is queried with that subject protein. From the table of bidirectional best hits, it is possible to select orthologs and align them with clustalW in one click.

One-click links to tools for finding motifs and signal sequences are provided at the bottom of each protein page. These tools include TMpred, PSORT, and PPSearch, which locate transmembrane regions, predict cellular localization, and find signature amino acid patterns. There is also a link to NCBI's Position Specific Iterated BLAST (Psi-BLAST), which may discover protein family relationships among proteins with fairly low overall sequence similarity.

Tools for comparative analysis of protein context will allow you to examine both the genetic and functional context of your chosen protein.

Two environments are offered for examining the genetic context of any protein. One familiar environment is GBrowse, the generic genome browser tool developed for the GMOD project and implemented in many model organism databases. The NMPDR protein page provides a rich environment for comparative analysis. Every protein in NMPDR is displayed in a table and a graphic centered on the focus peg flanked by its neighbors within about 8 kb upstream and downstream on the chromosome. Moreover, the colors of the flanking proteins in the graphic correspond to their functional clustering score. Red proteins are simply near by, while the relative proximity of the blue proteins is conserved in other genomes, which implies a functional relationship.

To compare the genetic context of the focus protein with the five most homologous genomes, simply click on "Show Compare Regions." The colors of the genes in this display are shared among homologs in the different genomes, and the numbers are the rank-ordered frequency of co-localization with the focus peg, which is red. The number of genomes and the size of the regions displayed may be adjusted in this tool. To view the maximum number of homologous regions, click the PINS button.

Finally, the functional context of the focus gene may be explored by comparing protein families and by looking at subsystems. If a curator has added the focus protein to a subsystem, a link to the populated subsystem spreadsheet is provided.

Comparative analysis of all proteins in whole genomes is made possible by the Signature genes tool, linked in the left navigation pane. This tool will allow you to find proteins in common to two sets of genomes, or those that discriminate one genome from another. Keywords may also be included to narrow the search, for example, to all kinases shared by a group of genomes. The output may be sorted by protein function, and is downloadable as a tab-deliminated table for use with Excel.