SP2ALIGN 1.0 – Protein Sequence Alignment using Weighted Profiles of Biochemical Properties

SP2ALIGN 1.0

:: DESCRIPTION

SP2ALIGN is a software and a web-server for pair-wise alignment of amino acid sequences by using weighted profiles of biochemical properties. This web-server finds an optimal global alignment of two amino acid sequences by utilizing weighted profiles of their biochemical properties instead of a single similarity matrix.

::DEVELOPER

Igor B. Kuznetsov, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • C++ Compiler

:: DOWNLOAD

 SP2ALIGN

:: MORE INFORMATION

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

 No

:: 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.

CONTRAlign 2.01 – CONditional TRAining for Protein Sequence Alignment

CONTRAlign 2.01

:: DESCRIPTION

CONTRAlign (CONditional TRAining for Protein Sequence Alignment)is an extensible and fully automatic parameter learning framework for protein pairwise sequence alignment based on pair conditional random fields. The CONTRAlign framework enables the development of feature-rich alignment models which generalize well to previously unseen sequences and avoid overfitting by controlling model complexity through regularization.

CONTRAlign Online Version

::DEVELOPER

Chuong Do (chuongdo@cs.stanford.edu)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 CONTRAlign

:: MORE INFORMATION

Citation

Do, C.B., Gross, S.S., and Batzoglou, S. (2006)
CONTRAlign: Discriminative Training for Protein Sequence Alignment.
In Proceedings of the Tenth Annual International Conference on Computational Molecular Biology (RECOMB 2006).