Computing Resources, Research Tools and Applications

Computing Resources

 

Computing Resources

Bioinformatics Computational Cluster
The Bioinformatics Department provides computational resources and support services for students, researchers, and faculty within the department. Support services include local desktop support, hardware/software purchasing, and computational support. Contact bioinfo-it@bu.edu with questions or to request help.

Spartan Cluster ›

The Spartan cluster is available to Bioinformatics students and researchers. The cluster consists of 360 processor cores and 30 terabytes (TB) of shared storage. The Spartan cluster was purchased with funding from a NSF CISE Computing Research Infrastructure (CRI) grant awarded in 2007.
Additional Resources Available to Bioinformatics Researchers at BU
New teraflops GPU cluster facility at BU
Massachusetts Green High Performance Computing Center (MGHPCC)

 

Tools and Applications for Public Use

 

Database Applications


GeneChords
Retrieve conserved gene cluster data from a number of microbial genomes as well as perform searches
based on genomic context
GENEVA
Catalogues SVGs (segmentally variable genes) in several complete microbial genomes.
HuGE Index
Database of gene expression in normal human tissues
Inverted Repeats Finder
Public repository of information on inverted repeats in genomic DNA
ORChID
The ∙OH Radical Cleavage Intensity Database (∙ORChID) stores hydroxyl radical cleavage data of DNA
sequences
Operons
Functional Gene Clusters, Operons with applications to bacterial microarray analys, pathway
reconstruction, functional annotation, system biology based on graph matching
Optimus
Retrieve conserved gene cluster data from a number of microbial genomes as well as perform searches
based on genomic context
Predictome
Tool for visualizing the predicted functional associations among genes and proteins in many different
organisms
Tandem Repeat Database
Public repository of information on tandem repeats in genomic DNA
VisANT
Web‐based software framework for visualizing and analyzing many types of networks of biological
interactions and associations
ELISA
Evolutionary Lineage Inferred from Structural Alignment


DNA/RNA Sequences


Cluster‐Buster
Program for finding clusters of pre‐specified motifs in nucleotide sequences
Comet
Cluster Of Motifs E‐value Tool finds statistically significant clusters of motifs in a DNA sequence
Cister
Cister predicts regulatory regions in DNA sequences by searching for clusters of cis‐elements.
Clover
Find overrepresented motifs in DNA sequences
CompAlign
Employs the mechanisms of string matching and string comparison yet avoids the overdependence of
those methods on position‐by‐position matching
FastER
Identification of genes with fast‐evolving regions in closely related genomes
GEMS
Gene Expression Module Sampler biclustering based on a Gibbs sampling paradigm
GLAM
Gapless Local Alignment of Multiple sequences: program for discovering functional motifs shared by a
set of nucleotide sequences
MotifViz
Integration of tools for detecting overrepresented motifs
RANKGENE
Program for analyzing gene expression data, feature selection and ranking genes based on the predictive
power of each gene to classify samples into functional or disease categories
ROVER
Find relatively overrepresented motifs in DNA sequences
SeqVISTA
A viewer of sequences and their annotations; now with a Motif module for integrating transcriptional
regulation analysis tools
Tractor
Program to computationally identify transcription factors with over‐represented binding sites in the
upstream regions of co‐expressed human genes


Gene Regulation


Carrie
Generate transcriptional regulatory networks from microarray and promoter sequence data.
CisML
An XML format for Sequence Motif Detection Programs.
Cis‐element info
Count matrices and background info for some /cis/‐elements.
ICSF
Identifies conserved structural features at sequentially degenerate locations in transcription factor
binding sites.
Possum
Simple matrix‐based motif search
Promoser
Human, mouse and rat promoter extraction service
REPFIND
Find clustered, exact repeats in nucleotide sequences
Site2genome
Locate sites in the human, mouse and rat genomes


Protein Engineering


K2
A genetic algorithm‐based protein structure alignment tool
FAST
A newer protein structure alignment tool, based on graph theory
SMM
A matrix‐based algorithm for predicting peptides binding to Major Histocompatibility Complex
ZDOCK
Rigid‐body protein‐protein docking software, using a Fast Fourier Transform search algorithm
RDOCK
A refinement method to minimize energy and re‐rank ZDOCK predictions
Docking Benchmark
A large set of test cases for evaluating the performance of docking algorithms
ZDOCK Conv3D
ZDOCK optimized with a new convolution library, resulting in improved speed and less memory usage
ZDOCK Server
An automated server for running ZDOCK, with capabilities for blocking and filtering contact residues


Other


Transcription Factor Binding Prediction Tools
BSG Graphical Theoretical Prediction of Transcription Factor Binding Sites
SVMotif A SVM Based Transcription Factor Binding Motif Finder
TFSVM Transcription Factor Binding Site Detection by Machine Learning

Cellular Metabolism
OHMICS Oral Human Microbiome Integrated Computational System