Version 2 beta 2 release

TF classifier
Local TFBS scan
Interface improvements
New family models and calibrated TF profiles
Bug fixes and stability improvements

Full Changelog: v2b1...v2.0b2

Version 2 beta release

• Updates to match changes of online services used
• Many TFBS profiles improved, new ones added
• Bug fixes and stability improvements

Version 2 second alpha release

• Total genome-wide TFBS annotation (almost fully automated)
• More TF family models, including those with two DBDs and non-HTH (now covering 27 major TF families)
• More calibrated TFBS profiles
• Multiple stability and usability improvements

Version 2 alpha release

De novo TFBS search pipeline is essentially complete. Double clustering approach eliminates redundancy more efficiently and results in better TFBS motif inference. The attached Mac and Linux binaries are 64-bit.

Version 2 development release 2

This development version eliminates online pfam search from de novo TFBS inference protocol making it faster and more reliable. It also includes a bunch of pre-calibrated CR tag based TFBS profles, mostly derived from RegPrecise.

Pre-release of version2

This is pre-release of version 2 which adds de-novo TFBS inference based on modified algorithm of Sahota and Stormo (DOI:10.1093/bioinformatics/btq501). Current implementation is very rough and without documentation, but the basic functionality is here.

Proper operation of version 2 requires fully working MEME Suite installation on the user system (necessary for generation of html output). The path in the Settings window should point to the system version of meme (rather than the one included in the distribution).

The binaries included are for OS X and 64 bit Linux. There won't be 32 bit Linux version. We'll think about Windows version later in the development.

All features of version 1 are retained with only minor bug fixes and modifications demanded by the switch of NCBI and EBI servers to the https protocol.

Version 1.0.4

Improvements in this release:

• NCBI server access restored (was broken since NCBI switch to https protocol),
• Updated python scripts to work with latest Biopython,
• Minor bug fixes.

Version 1.0.2

This release adds new Pectobacterium/Dickeya-specific profiles from RegPrecise 4.0 and recently updated P. atrosepticum 21A genome resulting in 102 Pectobacterium/Dickeya and 39 (as before) for Pseudomonadaceae. It also has minor bug fixes for Windows.

minor bugfix/improvements

This minor release contains the following improvements:

• a bug with annotation editing fixed,
• improved behaviour of the -i option in post-processing (HmmGen and MastGen) scripts,
• changed HMMER search results display on Windows and 32-bit Linux back to proper html format, as after the latest update HMMER web server produces compatible pages again.

version 1.0

First official release