The meta-CATS metadata genome comparison tool takes sequence data and determines the aligned positions that significantly differ between two (or more) user-specified groups. Once an analysis is started, a multiple sequence alignment is performed if the input was unaligned (such as from a database query). A chi-square test of independence is then performed on each non-conserved column of the alignment, to identify those that have a non-random distribution of bases. A quantitative statistical value of variation is computed for all positions. Columns that are perfectly conserved will not be identified as statistically significant. All other non-conserved columns will be evaluated to determine whether the p-value is lower than the specified threshold value. Terminal gaps flanking the aligned sequences will not be taken into account for the analysis.
This module is a component of the BV-BRC build system. It is designed to fit into the
dev_container infrastructure which manages development and production deployment of
the components of the BV-BRC. More documentation is available here.
There is one application service specifications defined here:
- Meta_CATS: The Meta-CATS tool looks for positions that significantly differ between user-defined groups of sequences.
The code in this module provides the BV-BRC application service wrapper scripts for the Meta-CATS service as well as some backend utilities:
| Script name | Purpose |
|---|---|
| App-MetaCATS.pl | App script for the Meta-CATS service |
Pickett, B. E., et al. "Metadata-driven comparative analysis tool for sequences (meta-CATS): an automated process for identifying significant sequence variations that correlate with virus attributes." Virology 447.1-2 (2013): 45-51.