Bioinformatics @Hamilton

Hamilton Bioinformatics Portal

* Overview

Bioinformatics is one of the hottest items in biology research today. Bioinformatics techniques can be applied to a wide variety of fields such as molecular medicine, gene therapy, drug development and evolutionary studies.

The Hamilton College Bioinformatics Portal is a server to run bioinformatics applications through a web-based interface called iNquiry. This interface integrates over 200 commonly used programs and allows the user to submit jobs to the server from anywhere, then retrieve the results at a later time. Having this resource on campus opens up new and exciting research possibilities for the entire Hamilton community.


* Access and Usage - Students and Faculty may use the Hamilton Bioinformatics Portal for research and projects.


* Cluster Hardware - The Hamilton Bioinformatics Portal consists of 8 dual processor (2 Ghz) Xserve G5 servers. Each server has 2 GB of RAM. Storage space totaling 750 GB is used for blast databases and research results. The cluster is connected via gigabit ethernet, both between the cluster nodes and to the Hamilton Network, to allow for the speedy transfer of the often large input and output files used in bioinformatics research activities.


* Hamilton Bioinformatics Portal Software List

A parallel version of NCBI blastall
The Bioteam

A general purpose multiple sequence alignment program
European Bioinformatics Institute

Parallel version of clustalW
Singapore Bioinformatics Institute

Emboss 2.8.0
Over 100 programs for sequence alignment, display, manipulation, and phylogeny.

A system for finding genes in microbial DNA
The Institute for Genomic Research

A package of programs for biological sequence analysis using profile hidden Markov models
HMMer Home

MrBayes is a program for the Bayesian estimation of phylogeny.
MrBayes Home

NCBI Tools
Blast tools from NCBI (Blastall, bl2seq, psiblast, phiblast, blast2cours)

A program package for phylogenetic analyses of DNA or protein sequences using maximum likelihood

PHYLIP is a free package of programs for inferring phylogenies
University of Washington

An integrated suite of software facilities for data manipulation, calculation and graphical display.
R Documentation

A package focused on comparisons of bio polymers, commonly DNA sequence and protein sequence
European Bioinformatics Institute