BioRG | Florida International University

Integrated Genomic Database

PseudoNEXUS is an integrated database storing a variety of information about five strains of the bacterium Pseudomonas aeruginosa (PAO1, PA14, PA2192, PAC3719, and PACS2).

PseudoNEXUS contains:

• Searchable entries for all genes & gene products in these organisms
• Tools to run versions of BLAST
• Tools to explore orthologs
• Tools to draw hydropathy plots for proteins
• Links from the entries to all major databases
• Advanced search capabilites

The work on this database was supported in part by an NIH/NIGMS grant S06 GM 08205.

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In biology the genome of an organism is its whole hereditary information and is encoded in the DNA (or, for some viruses, RNA). This includes both the genes and the non-coding sequences of the DNA. The term was coined in 1920 by Hans Winkler, Professor of Botany at the University of Hamburg, Germany. More precisely, the genome of an organism is a complete genetic sequence on one set of chromosomes. The term genome can be applied specifically to mean that stored on a complete set of nuclear DNA (i.e., the "nuclear genome") but can also be applied to that stored within organelles that contain their own DNA, as with the mitochondrial genome or the chloroplast genome. [ wikipedia ]

Search Databases

Select All PA01 PA14 PA2192 PAc3719 PACS2 [ Search Options ]

Blast Similarity Search Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences. A BLAST search enables a researcher to compare a query sequence with a library or database of sequences, and identify library sequences that resemble the query sequence above a certain threshold. [ wikipedia ] BLAST against the Pseudomonas databases

Hydrophobicity Plots A hydrophobicity plot is a quantitative analysis of the degree of hydrophobicity or hydrophilicity of amino acids of a protein. It is used to characterize or identify possible structure or domains of a protein. The plot has amino acid sequence of a protein on its x-axis, and degree of hydrophobicity and hydrophilicity on its y-axis. Analyzing the shape of the plot gives information about partial structure of the protein. [ wikipedia ] Use our hydrophobicity plot tool