Tuesday, December 21, 2004

Genomatix Suite 3.3 released

Today version 3.3 of Genomatix popular in silico promoter analysis suite got released. Notable quote from their mailing list press release :

"We are currently writing up a paper about a very promising approach to micro array analysis, which has now many times proved to be successful in identifying small sets of co-regulated genes. The strategy includes identification of involved TF binding sites and framework construction leading to regulatory network analysis. If you would like to know more on that, just let me know. I can send you a explanatory Powerpoint presentation."

Can't wait to see what its about... Microarray analysis would greatly benefit from a biologically accurate co-regulation analysis package. It would help to build hypothesis about regulation mechanism (which transcription factor is likely to be involved, which signalization cascade, which receptor / pathway, etc). Changelog available in the full post for those who are interested.

New features and main changes from Release 3.2:
ElDorado / Gene2Promoter

* New genomes:
o Canis familiaris (Genomatix build 1)
o Pan troglodytes (Genomatix build 1)
* Comparative Genomics includes chicken, dog, and chimpanzee in addition to human, mouse, and rat.
* Gene2Promoter allows input of gene names. Optionally, all orthologous genes can be included in the output.


* Shorter startup time, reduced memory usage and increased filter speed.
* Improved graph layout algorithm for large cluster layouts.
* Search for MeSH identifiers in BiblioSphere filters enabled.
* Comparative Genomics analysis can be started from gene context menu.
* New feature "Show/hide ghosts": input genes that don't comply with filter criteria (ghosts) can be hidden.
* Preselection of most likely candidate in ambiguous gene lists.
* Input of larger gene lists (up to 1000 genes) supported.

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