Entrez Programming Utilities (E-Utils)

PubChem

GenePlot

New NLM Catalog in Entrez

New Genome Builds

New Microbial Genomes in GenBank

Whole Genome Shotgun Project

Web BLAST

Trace Archive Grows

New Organisms in UniGene

RefSeq Version 8

Submissions Corner

Predicted Records

GenBank Release 144

BLAST 2.2.10

Publications

Masthead

GenePlot

Entrez Genome offers a new pairwise comparison tool called GenePlot to visualize similarities among bacterial genomes. Support for fungal genomic comparisons is also planned. To construct a GenePlot, genes are numbered sequentially along the genomic sequences of two organisms and the two corresponding sets of predicted proteins are compared using BLAST. For every case in which a pair or proteins, one from each genome, are mutual best matches, a point is plotted using the indices of the equivalent gene in the two genomes as the X and Y coordinates. Use the GenePlot link from an organism’s genome record to see a GenePlot against the organism with which it shares the highest number of reciprocal best hits. Comprisons between other organisms can be made using pull-down menus.

Figure 1 shows a GenePlot display for the comparison of two strains of Helicobacter pylori. An area of focus can be selected by centering the grey cross-hairs with the mouse. The width of the cross-hairs is determined by the zoom level set using the zoom control prior to clicking on the rightmost "close-up" plot. Best-hit pairs visible in the close-up plot are listed below with links to Blink reports for each protein in a pair as well as BLAST2 Sequences pairwise alignments. Use the "save" link to save a table listing all the pairwise best hits.

For nearly identical genomes, the GenePlot consists of a diagonal line running from the lower left to the upper right-hand corners. Closely related genomes may have undergone rearrangements, however, and these are seen as segments displaced from, or running perpendicular to, the main diagonal. Figure 2 shows a case in which two genomic segments from strains of Helicobacter pylori are displaced from the main diagonal with a perpendicular orientation. This indicates both a juxtaposition of the two segments but also a reversal of their orientations between the two genomes.

Figure 1: Full GenePlot display showing overview and close-up plots, genome selection pulldown menus, zoom control, gene list, and links to the data in tabular form and BLAST2Sequences displays of pairwise protein alignments.

Figure 2 : GenePlot comparison of proteins from two strains of Helicobacter Pylori, 26695 and J99. Each point represents a pair of proteins from the two organisms showing a symmetrical best BLAST score; the coordinates of each point correspond to the position of the protein genes in the two genomes. Note the juxtaposition and inversion of two segments of the genome between the two strains. Grey cross-hairs indicate the region displayed in the close-up plot, visible in Figure 1.

—DW