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Visit our Solutions page for product highlights. 2000;25:2529. Rebholz-Schuhmann D, Kirsch H, Arregui M, Gaudan S, Rynbeek M, Stoehr P. 2003;75:46464658. Acids Res. These lists may be in any of three currently supported formats: plain text lists of proteins (ASCII format), Mascot database search results (.dat format), or protXML results (XML format) obtained from Protein Prophet13 using the Trans Proteomic Pipeline (TPP)14,15 (tools.proteomecenter.org/software.php). Selecting pie-chart rendering allows for display of each major category of GO term (biological process, cellular component, and molecular function) as shown in Figure 4. We chose to integrate STRAP with Gaggled programs to increase the overall utility of STRAP and allow for incorporation within open-source proteomics workflows which make use of the TPP.AnnotationsSTRAP parses protein annotation information from XML data in the online UniProtKB database. Click This Button Click This Button Click This Button . Keller A, Eng J, Zhang N, Li XJ, Aebersold R. All columns in the main annotation table, including the GO category column allow sorting. 2007;35:W193W200. Bhatia, David H. Olason PI. In addition to the full annotation display of GO term attributes obtained from the on-line database, users can manually edit these terms within STRAP as necessary if a user has additional expert information about the proteins of interest. Nucleic Acids Res. Nat Genet. These results then may be stored in the STRAP atxt file.Figure 3STRAP’s built in Gene Ontology Term Browser. Input files for STRAP must contain protein entry or accession numbers in the UniProt Knowledgebase (www.uniprot.org) format (e.g., HBBHUMAN, or P002833).
For this reason, it is important for any protein annotation software to have capabilities to compare protein sets. In addition to showing the number of GO annotations, a percentage value is listed to indicate the fraction of GO terms that is represented out of the complete list of GO annotations for the entire set of proteins. [PubMed]9. Current version of Scaffold available (4.7.5). BMC Bioinformatics. Kaplan N, Vaaknin A, Linial M. Some content may be unavailable. REFERENCES1. Nucleic Acids Res. 2004;32:D115D119. [PMC free article] [PubMed]11. Shannon PT, Reiss DJ, Bonneau R, Baliga NS. 2008;10:604617. A complete description of GO terms sub-category may be found in the Supplemental Table 1 (A–C) under the main category to which they belong. Here we present the Software Tool for Researching Annotations of Proteins (STRAP) – a user-friendly, open-source C# application. Bioinformatics. Bare JC, Shannon PT, Schmid AK, Baliga NS. ea41d647aa
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