SQUARE – Server for Quick Alignment Reliability Evaluation

SQUARE

:: DESCRIPTION

SQUARE (the Server for Quick Alignment Reliability Evaluation) is a Web-based version of the method we developed to predict regions of reliably aligned residues in sequence alignments. Given an alignment between a query sequence and a sequence of known structure, SQUARE is able to predict which residues are reliably aligned. The server accesses a database of profiles of sequences of known three-dimensional structures in order to calculate the scores for each residue in the alignment.

::DEVELOPER

STRUCTURAL COMPUTATIONAL BIOLOGY GROUP

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 No

:: MORE INFORMATION

Citation

Tress ML, Graña O, Valencia A.
SQUARE–determining reliable regions in sequence alignments.
Bioinformatics (2004 Apr). Vol 20, Issue , 974-975

WebGimm – Cluster Analysis Server

WebGimm

:: DESCRIPTION

WebGimm is a Java Web Start based tool for performing gene and sample clustering analysis of microarray data and enrichment analysis on the results of clustering. WebGimm operates on the client-server paradigm and offloads the burden of computation from the user’s machine to our servers.

:: DEVELOPER

Laboratory for Statistical Genomics, Univ. Cincinnati

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/MacOsX/Windows
  • Java

:: DOWNLOAD

 WebGimm

:: MORE INFORMATION

Citation:

Source Code Biol Med. 2011 Jan 17;6:3.
WebGimm: An integrated web-based platform for cluster analysis, functional analysis, and interactive visualization of results.
Joshi VK, Freudenberg JM, Hu Z, Medvedovic M.

PROMALS3D – Multiple Sequence and Structure Alignment Server

PROMALS3D

:: DESCRIPTION

PROMALS3D (PROfile Multiple Alignment with predicted Local Structures and 3D constraints) constructs alignments for multiple protein sequences and/or structures using information from sequence database searches, secondary structure prediction, available homologs with 3D structures and user-defined constraints.

::DEVELOPER

Grishin Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /MacOsX
  • C++ Compiler
  • python
  • awk

:: DOWNLOAD

 PROMALS3D

:: MORE INFORMATION

Citation:

PROMALS3D: a tool for multiple sequence and structure alignment.
Jimin Pei, Bong-Hyun Kim and Nick V. Grishin.
Nucleic Acids Res. 2008 36(7):2295-2300.

MDCS – Microarray Data Classification Server

MDCS

:: DESCRIPTION

The MDCS provides maximal margin Linear Programming method (Antonov et al., 2004) for classification of tumor samples based on microarray data. This procedure detects groups of genes and constructs models (features) that strongly correlate with particular tumor types. The detected features include genes whose functional relations are changed for particular cancer types.

::DEVELOPER

MDCS Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 MDCS

:: MORE INFORMATION

Citation:

Antonov, A.V., Tetko, I.V, Prokopenko, V.V., Kosykh,D. & Mewes, H.W.
Web Portal for Classification of Expression Data using Maximal Margin Linear Programming,
Bioinformatics, 2004, 20, 3284-5.

 

BioconductorBuntu – Web-Based DNA Microarray Analysis Server

BioconductorBuntu

:: DESCRIPTION

BioconductorBuntu is a custom distribution of Ubuntu Linux that automatically installs a server-side microarray processing environment, and provides a user friendly web-based graphical user interface to many of the tools developed by the Bioconductor Project, whether locally or across a network. Installation is a turn-key procedure, simply based on booting off the installation CD or image file. In its current version, several microarrays analysis pipelines are supported including oligonucleotide (e.g. Affymetrix Genechips), dual or single dye (e.g. Exqion miRNA arrays) experiments, with the existing set of preprocessing methods for normalization, background correction and so on are easily expanded.

::DEVELOPER

School of Mathematics, Statistics & Applied Mathematics 
National University of Ireland Galway, University Road

:: SCREENSHOTS

:: REQUIREMENTS

  • bootable CD-ROM drive

:: DOWNLOAD

  BioconductorBuntu iso image

:: MORE INFORMATION

Citation

Paul Geeleher, Dermot Morris, John P. Hinde and Aaron Golden
BioconductorBuntu – A Linux Distribution that Implements a Web-Based DNA Microarray Analysis Server
Bioinformatics (2009) 25 (11): 1438-1439