Genomica Genome Browser

Category Genomics>Genetic Data Analysis/Tools

Abstract The Genomica Genome Browser allows you to visualize data in chromosomal coordinates, similar to common web genome browsers but with expanded viewing capabilities.

More importantly, Genomica provides a suite of statistical analysis tools that perform statistical comparisons between data that is represented in 'chromosomal coordinates'.

1) Visualizing results --

All the data is represented in 'chromosome tracks'.

The tracks are quite diverse in terms of the different objects that they can represent.

For example, the ‘sample tracks’ that come with Genomica include tracks for displaying: 'colored boxes' (e.g., useful for representing genes); graphs; impulse graphs; ovals; and colored bar graphs (e.g., useful for representing ‘tiling expression’ measurements).

After loading an expression file into Genomica, you can load '(gxt) track files' using the 'Chromosome' --> 'Load Track From File...' or the 'Chromosome' --> 'Load Track From Repository...' menu.

Using the control panel within the chromosome viewer, you can:

• a) navigate to the exact locations you want to view;
• b) select a single or multiple chromosome display and control which chromosomes will be displayed;
• c) select which tracks will be displayed and change the visual properties for each track;
• d) search for items within the tracks loaded;
• e) view the items in each track as a table; and
• f) print the current view into an image.

2) Loading your own track --

You can also load your own tracks into Genomica.

The format is quite simple and you can use provided examples as a guideline.

The format is Extensible Markup Language (XML), but the data part is tab-delimited with one line for each item displayed, with the following columns for each item:

• Column 1: Chromosome name;
• Column 2: Unique identifier;
• Column 3: Start coordinates (in base pairs);
• Column 4: End coordinate (in base pairs);
• Column 5: Index of the feature type (a number between zero and the number of types minus 1);
• Column 6: Real-valued number.

This data part is wrapped by an XML header. The XML contains various display properties of the track.

All of these can be controlled visually within the Genomica Graphical User Interface (GUI) so you do Not need to use them when creating your own tracks.

However, one field is important to fill in, and this is the "FeatureTypes" field.

3) Browsing a chromosome track as a table --

A very useful feature that the manufacturer implemented in Genomica's Genome Browser is the ability to traverse all the items of a particular chromosome track as a spreadsheet-like table, while in parallel seeing in the chromosome viewer, what the region around the selected chromosome item looks like.

In this way, you can for instance load several tracks and display only the genes in the table view, such that clicking on each gene will then show all the data in the chromosome viewer that appears in the ‘gene area’ and some selected number of 'base pairs' flanking the gene.

As another example, when analyzing ChIP-chip data, you can select a table view on regions that are 'called' as significantly bound by some analysis program, and browse the items in the table, each time viewing the data that supports the call that was made in that region of the chromosome in which the call for significant binding was made.

Note: See G6G Abstract Number 20340 for additional product info from this manufacturer.

System Requirements

Contact manufacturer.

Manufacturer

• Developed by Yaniv Lubling and Eran Segal at the
• Segal Lab of Computational Biology
• Weizmann Institute of Science
• Rehovot, 76100
• Israel

Manufacturer Web Site Genomica Genome Browser

Price Contact manufacturer.

G6G Abstract Number 20341

G6G Manufacturer Number 104001