Research Tools and Applications

Below you will find several categories of computational research tools, databases and applications developed by members of the BU Bioinformatics community.

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

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

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

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, and 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

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

OHMICS Oral Human Microbiome Integrated Computational System