Email updates

Keep up to date with the latest news and content from BMC Bioinformatics and BioMed Central.

Open Access Highly Accessed Software

GOmotif: A web server for investigating the biological role of protein sequence motifs

Franklin Bristow13, Runtao He12 and Gary Van Domselaar123*

Author Affiliations

1 National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, R3E 3R2, Canada

2 Department of Medical Microbiology, School of Medicine, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada

3 Department of Computer Science, University of Manitoba, R3T 2N2, Winnipeg, MB, Canada

For all author emails, please log on.

BMC Bioinformatics 2011, 12:379  doi:10.1186/1471-2105-12-379

Published: 26 September 2011

Additional files

Additional File 1:

Overall Average Sensitivity and Specificity. This spreadsheet reports the overall specificity and sensitivity calculated for each of the three biological domains (molecular function, biological process and cellular component). This spreadsheet provides a high-level overview of the data contained in the remaining additional files 2, 3 and 4.

Format: XLS Size: 28KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional File 2:

Node selection report for Biological Process. A report of the fine-grained details about how sensitivity and specificity were calculated for Biological Process. Column A (Allowed Distance) reports the allowable distance from the correct GO term that can be reported as a true positive. Column B (PROSITE ID) reports the PROSITE database identifier that provided these results. Column C reports the PROSITE pattern record for this PROSITE ID, and column D reports the length of the PROSITE pattern. Column E (All Selected) reports the total number of GO terms that were selected by our selection algorithm. Column F-I (True Positives, True Negatives, False Positives, False Negatives) reports the total number of GO terms selected that match the criteria for true positive, false positive, true negative or false negative. Columns J and K (Specificity and Sensitivity) report the calculated specificity and sensitivity for the data in the row.

Format: XLS Size: 2.3MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional File 3:

Node selection report for Molecular Function. A report of the fine-grained details about how sensitivity and specificity were calculated for Molecular Function. Column A (Allowed Distance) reports the allowable distance from the correct GO term that can be reported as a true positive. Column B (PROSITE ID) reports the PROSITE database identifier that provided these results. Column C reports the PROSITE pattern record for this PROSITE ID, and column D reports the length of the PROSITE pattern. Column E (All Selected) reports the total number of GO terms that were selected by our selection algorithm. Column F-I (True Positives, True Negatives, False Positives, False Negatives) reports the total number of GO terms selected that match the criteria for true positive, false positive, true negative or false negative. Columns J and K (Specificity and Sensitivity) report the calculated specificity and sensitivity for the data in the row.

Format: XLS Size: 2.3MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional File 4:

Node selection report for Cellular Component. A report of the fine-grained details about how sensitivity and specificity were calculated for Cellular Component. Column A (Allowed Distance) reports the allowable distance from the correct GO term that can be reported as a true positive. Column B (PROSITE ID) reports the PROSITE database identifier that provided these results. Column C reports the PROSITE pattern record for this PROSITE ID, and column D reports the length of the PROSITE pattern. Column E (All Selected) reports the total number of GO terms that were selected by our selection algorithm. Column F-I (True Positives, True Negatives, False Positives, False Negatives) reports the total number of GO terms selected that match the criteria for true positive, false positive, true negative or false negative. Columns J and K (Specificity and Sensitivity) report the calculated specificity and sensitivity for the data in the row.

Format: XLS Size: 2.3MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data