 |
This is a one-stop downloading site that searches popular online CAT libraries and provides relevant CATs to a particular clinical topic.
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| Cellware |
Cellware has not only
been designed to conduct modeling and simulation of gene
regulatory and metabolic pathways but also offer an integrated
environment for diverse mathematical representations, parameter
estimation and optimization. In addition, a user-friendly
graphical display and capability to run large and complex
models would be provided by default. A very special feature
of Cellware is that it would be the first grid based modeling
and simulation tool in the field of Systems Biology, to our
best knowledge. |
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Clustalw
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Clustal W is a general
purpose multiple sequence alignment program for DNA or proteins.
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| ClustalW-MPI |
ClustalW is a tool
for aligning multiple protein or nucleotide sequences. The
alignment is achieved via three steps: pairwise alignment,
guide-tree generation and progressive alignment. ClustalW-MPI
is a distributed and parallel implementation of ClustalW.
All three steps have been parallelized to reduce the execution
time. The software uses a message-passing library called
MPI (Message Passing Interface) and runs on distributed workstation
clusters as well as on traditional parallel computers. |
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| CMDWave |
Predicting Conserved Motifs in Protein Sequences using Wavelet Transforms. |
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EMBOSS
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The European Molecular
Biology Open Software Suite - EMBOSS is a package of high-quality Open
Source software for sequence analysis. |
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Ensembl Genome Browser
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Ensembl is a joint project between EMBL - EBI and the Sanger Centre to
develop a software system which produces and maintains automatic annotation
on eukaryotic genomes. |
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| ExTRS |
Exhaustive Tandem Repeats Search Algorithm.
Downloads [ExTRS IA-32 Version, ExTRS IA-64 Version, ExTRS Solaris Version] |
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| GridBlast |
GridBlast is a grid-enabled, high-throughput "task farming" application used to distribute work over geographically distributed, nodes on a grid, for BLAST runs.
Downloads [GridBlast_v1.3.tar.gz] |
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| GridX |
This project intends to develop a general-purpose meta-scheduler for grid applications incorporating both the economic as well as the performance aspects. |
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| inGRD |
Inter Network Grid Resource Discovery Framework.
Download [ingrd_v0.8.1.tar.gz] |
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Integrated Haplotype Analysis Pipeline
 |
A tool for inferring haplotype blocks and selecting tag SNPs using genotype data from the International HapMap Project. This tool utilizes HapBlock as the backend haplotyping tool. |
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InterProScan
 |
A tool that scans
given protein sequences against the protein signatures of the InterPro
member databases. |
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| MiRTif: MicroRNA:Target Interaction Filter |
A machine learning algorithm based on SVM (support vector machine) that serves as a post-processing filter for the miRNA. |
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| Protein Subcellular Localization Prediction for Gram-negative Bacteria |
Subcellular localization is crucial for determining the functions of proteins. This web-based tool, P-CLASSIFER, is used to predict subcellular localization for Gram-negative bacteria. P-CLASSIFIER is built on top of multiple support vector machines. |
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| pSLIP |
Prediction of Subcellular Localization in Proteins. |
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SingBLAST
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Sequence
Manipulation Suite
 |
A suite of web-based
programs for analyzing and formatting DNA and protein sequences. |
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Sequence
Retrieval System
 |
Sequence Retrieval
System for searching and retrieving sequence information from various
databases. |
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| SCATTER |
SCATTER is a "task farming" program used to distribute work over a
cluster for BLAST runs. SCATTER was developed as part of the NCC project for
providing high throughput BLAST capabilities. The program is a freeware and
can be copied and used by anyone. However, I would appreciate it if you could
mention the Copyright Information if you do happen to make any changes to it.
It would be remiss of me if I didn't mention the names of Raphael Clifford
(Imperial College) and Aaron Mackey (University of Virginia) who have developed
a similar software called Disperse. The idea for SCATTER was based on their work.
I had some problems getting Disperse to work and hence chose to write my own
application. I would like to thank Aaron and Raphael for access to their software.
Downloads [Scatter_v1-0-1.tar.gz, Scatter_v1-0-2.tar.gz] |
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UCSC
Genome Browser
 |
UCSC Genome browser
mirror of various organisms. |
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| WebAllergen |
Predicting Allergenic Proteins. |
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| Wildfire |
Wildfire is a graphical tool for building workflows. It comes preconfigured to use EMBOSS programs as components for Bioinformatics workflows, and is extensible to support other components. |
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Wisconsin
Package
(SeqWeb)
 |
A commercial sequence
analysis package that offers sequence and analysis result management
and sharing [get an account, FAQ, supported
browsers, application list].
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