News:

07/23/2008: Support for yeast genome has been added.

07/22/2008: Mouse mm9 genome database has been released.

04/10/2008: A function has been added under the “Genome” menu to summarize pairwise overlap among multiple lists of genomic regions.

03/23/2008: CisGenome can now support ChIP-seq data analysis. A collection of functions has been added and can be accessed under the “Sequencing” menu. Usage information can be found in the tutorials.

03/23/2008: CisGenome Browser has been updated. A few functions have been added to enhance its ability to configure multiple tracks simultaneously.

03/23/2008: Two functions have been added to support BAR file operations, including converting BAR files to text files, and retrieving signals from BAR files for a collection of specified genomic regions.

03/20/2008: A test version of Arabidopsis database has been posted. Please feel free to test it and report bugs to us.

10/31/2007: Users can now choose either CisGenome Browser or UCSC genome browser as the default browser. To set the browser, go to “Browser > Default Browser”.

10/31/2007: CisModule has been incorporated into CisGenome to perform de novo cis-regulatory module discovery. CisModule.exe is kindly provided by Qing Zhou.

10/29/2007: For a list of genomic regions, you can now get a summary of their distributional statistics, i.e., how many regions are located in exons, introns, UTRs, promoters, CDSs, etc.

10/29/2007: CisGenome can now convert a tab-delimited text file to a BAR tiling array project. Quantile normalization for text files is also offered. These two functions can help you analyze tiling array data generated from non-Affymetrix platforms (e.g., Agilent or NimbleGen arrays).

10/29/2007: CisGenome now provides a function to convert soft-masked FASTA files to hard-masked FASTA files (i.e., repeats are masked by N instead of a,c,g,t). This would allow you to export sequences to feed external software which may only recognize hard masked sequences.

10/16/2007: Support to Affymetrix’ new CEL file format has been added. CisGenome can now recognize CEL v3 (ASCII), CEL v4 (BINARY) and CEL in Command Console Format (BINARY).

09/30/2007: CisGenome (v1.0_beta) has been released. Welcome to play with it and report bugs to us!

CisGenome News