Intramural Research
Online Research Resources
MCS
|
Please use our new and improved WebMCS server at http://zoo.nhgri.nih.gov/mcs
You will be automatically taken there in 3 seconds.WebMCS
WebMCS is a tool that can be used to detect MCSs, or Multi-species Conserved Sequences, from multiple sequence alignments provided by you. The details of this method are provided in a manuscript by E.H. Margulies, M. Blanchette, NISC Comparative Sequencing Program, D. Haussler, and E.D. Green "Identification and Characterization of Multi-Species Conserved Sequences" Genome Research (13:2507-2518).
Submitting Data for MCS Analysis
Submit Data for MCS Analysis. Or first read a brief overview of the submission requirements:
Input
At a minimum, you must provide WebMCS with a multiple sequence alignment and your email address. Currently WebMCS only accepts MultiPipMaker alignments. Future versions will accept alignments from other programs. Once MCSs have been identified from your data, an email will be sent to you containing a URL with your results.
In addition, If you also submit an exons annotation file and/or a RepeatMasker file, WebMCS will determine the amount of overlap with annotated coding regions, UTRs, and/or ancestral repeats. Currently WebMCS accepts exon information in the PipMaker exons format or extracts this information from the UCSC Genome Browser using valid genome coordinates.
Output
WebMCS provides the results of detected MCSs in the form of UCSC Custom Tracks, as well as a number of ancillary files including a summary of detected MCSs, the computed conservation scores, identified genomic features, and others. The Custom Tracks file allows you to display your results within the UCSC Genome Browser.
- Submit Data for MCS Analysis.
- Additional Information about input requirements for WebMCS.
Overview
The process of identifying MCSs is accomplished by calculating a Multi-species Conservation Score (where higher scores represent more conserved regions). This Conservation Score is calculated in a fashion that weights the relative contribution of each species' sequence by accounting for its baseline neutral substitution rate (relative to the human reference sequence). Using this weighting scheme, conserved sequences from more diverged species make a greater relative contribution to the Conservation Score than those from less diverged species. WebMCS currently measures baseline neutral substitution rates at 4-fold degenerate positions. These are the third position of certain codons that can be any base and still code for the same amino acid.
MCSs are defined as a segment of contiguous sequence where each base exceeds a defined conservation score threshold. The default setting for WebMCS is to select a threshold such that MCSs include 5% of the reference sequence. This threshold is noted as the Conservation Score representing the 95th percentile.
Comments, suggestions and problems to bioinformatics@nhgri.nih.gov
