03/30/2011: hmChIP is released! Using >2000 publicly available ChIP-seq and ChIP-chip profiles to help you understand your own biological system now becomes easier than ever. You can study context-dependency of cis-regulatory elements and find collaborating proteins of your transcription factor of interest by taking advantage of public ChIP data from diverse cell types and for a variety of proteins. Check hmChIP database and web server here.
01/15/2011: CisGenome v2.0 is released! See Tutorial. This version contains a new ChIP-seq peak caller. The new peak caller is designed for experiments with both IP and control samples (i.e. two sample analysis). Features of the new algorithm include:
(1) It is more robust than the old peak caller, and it requires much less memory. Most of the memory issues in the old version will go away with the new algorithm.
(2) It is able to handle biological/technical replicates.
(3) One can now choose to use a dynamic read rate model which estimates background read sampling rate using a local window.
01/14/2011: New file conversion functions are added. CisGenome can now convert bowtie output to ALN file (which can be used for ChIP-seq peak calling). It also recognizes both old and new ELAND output formats now. A function that converts BAR to WIG is also added.
01/11/2011: A number of sample data sets are provided here.
03/04/2010: Genome database updates. Conservation scores for hg19 are added. Rat (rn4) is supported now.
11/11/2009: Genome database updates. Human (hg19), Dog (canFam2), Cow (bosTau4), Zebrafish (danRer4, danRer5), Arabidopsis (TAIR9) are now supported. CisGenome executable files are updated to supported this new genome assemblies.
4/22/2009: file_eland2aln has been updated to support new ELAND format -> ALN conversion. A tool for BED->ALN conversion (file_bed2aln) has been added.
4/22/2009: Support to Chicken and C. elegans genomes have been added.
2/20/2009: A number of users reported that the sorting function in GUI “ Sequencing > Alignment ->BAR” (tablesorter_str in Unix) often cannot run through due to insufficient memory. The function is updated now, and the new version is more memory efficient. It requires about 700Mb memory for the STAT1 test data posted on our website.
12/10/2008: Arabidopsis database has been upgraded to TAIR8. Some bugs are fixed.
11/02/2008: The paper describing CisGenome is published by Nature Biotechnology today. If you need to cite CisGenome in your own work, please refer to this paper.
11/02/2008: User manual page has been updated. Several commonly used analysis pipelines are listed for users who wish to run CisGenome as command line programs.
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!