CMTV
Comparative Map and Trait Viewer (CMTV) is an integrated bioinformatic tool to construct consensus maps and to compare QTL and functional genomics data across genomes and experiments.
CMTV offers the combination and subsequent graphic display for a variety of traits and environments, histograms of marker density and gene density, for the complete data set of inbred neighbors and local gene expression data. This way of representation facilitates the analysis of large datasets generated from many traits and/or experiments. The subsequent identification of consensus regions can be used in the design of marker assisted selection (MAS) experiments.
CMTV assists in investigating genetic regions with associations to a number of quantitative traits, located with the use of linkage and QTL likelihood data. CMTV integrates local data with public data, and combines these with genetic and functional information at choice. CMTV provides tools for easy handling large volumes of data, with better rules for simple map combination. CMTV can be used as a workbench for invoking sequence-based analysis programs.CMTV has the possibilty to examine the evolutionary fate of duplicated genes, by comparison of research QTL data with data from central public repository databases. The resulting composite maps for which common markers are found, thus reveal the presence of QTL reported for the same trait in other experiments, as well as the corresponding duplicated neighbouring regions of the genome. The absence of QTL in the duplicated region is suggestive of loss of function following the duplication event.
Users can select QTL at choice; data from public sources can be imported into the workspace to hunt for candidate genes in syntenic regions.CMTV offers the interpretation of sequence similarities on a genome-scale. The dynamically computed sequence similarity search results between two clones are displayed as red bars, with differents colored links for sequence matches on the same or opposite nucleotide strand. This type of display offers the possibility to detect inversions of homologous genes, repetitive elements and the conspicuous absence of gene homology.
The gathered data can by visualized in several (graphical) ways by CMTV during the analysis process.
The positional offsets and groupings of annotations on a genomic clone can be displayed. Table Viewer represents each datum as a row with its properties as columns, and the values rendered as text. With the ontology editor (DAGEdit) the Gene Ontology terms associated with the annotations, and their conceptual relationship to other biologically relevant terms, can be displayed.CMTV was originally developed by Andrew Farmer from NCGR. Generation Challenge Programme supported the development of CMTV as a stand alone tool. CMTV has been used to successfully to construct drought tolerance consensus maps for Maize at CIMMYT.
download CMTV from sourceforge
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