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Figure 3 | BMC Bioinformatics

Figure 3

From: Computational identification of strain-, species- and genus-specific proteins

Figure 3

Example output from CUPID. Helicobacter pylori 26695 was selected to retrieve proteins encoded only in bacteria of the Helicobacter genus. The results display protein accessions, name, length, family classification, uniqueness status, evidence for uniqueness, core status, other core proteins, and additional links. Accession links (first column) connect the protein to (i) the protein entry report, (ii) iProClass [24] entry report with rich links to over 90 molecular databases, and (iii) the UniProtKB report. Additional links (last column) are provided to (i) the EMBL DNA sequence (derived from the UniProtKB cross-reference), (ii) a pre-filled form for tBLASTn http://www.ncbi.nlm.nih.gov/BLAST/ for protein search against translated NCBI DNA databases (with Entrez post-processing set to filter out self hits) and (iii) signal sequence and transmembrane domain prediction using Phobius [25].

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