Tag: Recognition

ARTS 0.2 – Accurate Recognition of Transcription Starts in Human

ARTS 0.2

:: DESCRIPTION

ARTS is a novel kernel based method that accurately recognizes transcription start sites in human. The application of otherwise too computationally expensive Support Vector Machines was made possible due to the use of efficient training and evaluation techniques using suffix tries. In a carefully designed experimental study, we compare our TSS finder to state-of-the-art methods from the literature: McPromoter, Eponine and FirstEF. For given false positive rates within a reasonable range, we consistently achieve considerably higher true positive rates.

::DEVELOPER

Rätsch Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 ARTS

:: MORE INFORMATION

Citation

Bioinformatics. 2006 Jul 15;22(14):e472-80.
ARTS: accurate recognition of transcription starts in human.
Sonnenburg S, Zien A, Rätsch G.

TAXFOLD – Improve Toxonomy-based Protein Fold Recognition

TAXFOLD

:: DESCRIPTION

TAXFOLD is a new taxonomy-based protein fold recognition method. It extensively exploits the sequence evolution information from PSI-BLAST profiles and the secondary structure information from PSIPRED profiles. A comprehensive set of 137 features is constructed, which allows for the depiction of both global and local characteristics of PSI-BLAST and PSIPRED profiles.

::DEVELOPER

Chen Xin , Yang Jian-Yi

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 TAXFOLD

:: MORE INFORMATION

Citation

Jian-Yi Yang and Xin Chen,
Improving taxonomy-based protein fold recognition by using global and local features,
Proteins: Structure, Function, and Bioinformatics Volume 79, Issue 7, pages 2053–2064, July 2011

THREADER 3.51 – Protein Fold Recognition by Threading

THREADER 3.51

:: DESCRIPTION

THREADER is a software of threading which is an approach to fold recognition which used a detailed 3-D representation of protein structure. The idea was to physically “thread” a sequence of amino acid side chains onto a backbone structure (a fold) and to evaluate this proposed 3-D structure using a set of pair potentials and (importantly) a separate solvation potential.

:DEVELOPER

Bioinformatics Group – University College London

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 THREADER

:: MORE INFORMATION

Citation:

Jones, D.T., Miller, R.T. & Thornton, J.M. (1995)
Successful protein fold recognition by optimal sequence threading validated by rigorous blind testing.
Proteins. 23, 387-397.