ANGLE – Predict Coding Sequences in low quality cDNA

ANGLE

:: DESCRIPTION

ANGLE (Anti Noise Gene Locator Engine) is a new program for predicting coding sequences in low quality cDNA. To achieve error-tolerant prediction, ANGLE uses a machine-learning approach, which makes better expression of coding sequence maximizing the use of limited information from input sequences.

::DEVELOPER

Kana Shimizu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

ANGLE

:: MORE INFORMATION

Citation

Shimizu, K., Adachi, J., and Muraoka, Y. (2006)
ANGLE: a sequencing errors resistant program for predicting protein coding regions in unfinished cDNA.
J Bioinform Comput Biol 4, 649-664

I-Mutant 2.0.7 – A Tool for Predicting Protein Stability upon Mutation

I-Mutant 2.0.7

:: DESCRIPTION

I-Mutant is a support vector machine (SVM)-based tool for the automatic prediction of protein stability changes upon single point mutations. The software’s predictions are performed starting either from the protein structure or, more importantly, from the protein sequence.

::DEVELOPER

the Structural Bioinformatics Unit

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Mac / Windows
Python

:: DOWNLOAD

I-Mutant

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W306-10.
I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure.
Capriotti E, Fariselli P, Casadio R.

TreeDet v2 – Predicting Functional Residues in Protein Sequence Alignments

TreeDet v2

:: DESCRIPTION

The TreeDet (Tree Determinant) Server is the first release of a system designed to integrate results from methods that predict functional sites in protein families. These methods take into account the relation between sequence conservation and evolutionary importance. TreeDet fully analyses the space of protein sequences in either user-uploaded or automatically generated multiple sequence alignments. The methods implemented in the server represent three main classes of methods for the detection of family-dependent conserved positions, a tree-based method, a correlation based method and a method that employs a principal component analyses coupled to a cluster algorithm.

::DEVELOPER

the Bioinformatics Unit

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser (do not support IE)

:: DOWNLOAD

:: MORE INFORMATION

Citation

TreeDet: a web server to explore sequence space.
Carro A, Tress M, de Juan D, Pazos F, Lopez-Romero P, del Sol A, Valencia A, Rojas AM.
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W110-5.