Related Experiment Videos
Current Comparative Table (CCT) automates customized searches of dynamic biological databases
Benjamin R Landsteiner1, Michael R Olson, Robert Rutherford
1Department of Biology, St Olaf College, 1520 St Olaf Avenue, Northfield, MN 55057, USA.
Nucleic Acids Research
|June 28, 2005
Summary
Current Comparative Table (CCT) software automates bioinformatics searches for biologists, simplifying gene and ortholog identification. This tool highlights changes in sequence data, aiding daily research decisions.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Biologists increasingly require automated tools for complex bioinformatics searches.
- Managing and interpreting large datasets from sequence and HMM databases presents challenges.
Purpose of the Study:
- To introduce Current Comparative Table (CCT) software for automating customized bioinformatics searches.
- To provide biologists with an efficient tool for gene and ortholog identification.
Main Methods:
- Developed a web-based software program with a BioPerl core.
- Integrated support for BLAST, HMMER (hidden Markov model) searches, and other relevant bioinformatics tools.
- Implemented features for remote or local use on Mac OS X and Linux.
Main Results:
- CCT enables automation of customized searches against remote sequence and HMM databases.
- The software color-codes results by age and highlights subtle changes in sequence or annotation.
- Facilitates rapid examination of current results in context, influencing experimental design.
Conclusions:
- CCT empowers non-bioinformaticians to perform automated custom searches.
- The software enhances the efficiency of gene and ortholog identification for biologists.
- CCT streamlines the process from database submission to experimental application.