{"id":3585,"date":"2012-09-19T10:28:11","date_gmt":"2012-09-19T14:28:11","guid":{"rendered":"https:\/\/www.bu.edu\/bioinformatics\/?page_id=3585"},"modified":"2012-09-19T12:00:54","modified_gmt":"2012-09-19T16:00:54","slug":"research-tools-and-applications","status":"publish","type":"page","link":"https:\/\/www.bu.edu\/bioinformatics\/research-tools-and-applications\/","title":{"rendered":"Research Tools and Applications"},"content":{"rendered":"<h3>Below you will find several categories of computational research tools, databases and applications developed by members of the BU Bioinformatics community.<\/h3>\n<p><script type=\"text\/javascript\">\/\/ <![CDATA[\r\nif (document.getElementById) {\r\ndocument.writeln('<style type=\"text\/css\">') document.writeln('.texter {display:none} @media print {.texter {display:block;}}') document.writeln('\/\/<\/STYLE>') } function openClose(theID) { if (document.getElementById(theID).style.display == \"block\") { document.getElementById(theID).style.display = \"none\" } else { document.getElementById(theID).style.display = \"block\" } } \/\/ --&gt;]]><\/script><\/p>\n<div style=\"cursor: pointer;\" onclick=\"openClose('a1')\">\n<h2><a>Gene Regulation<\/a><\/h2>\n<p>\u00a0<\/p>\n<\/div>\n<div id=\"a1\" class=\"texter\">\n<p><a href=\"http:\/\/zlab.bu.edu\/CarrieServer\/html\/\">Carrie<\/a> Generate transcriptional regulatory networks from microarray and promoter sequence data<\/p>\n<p><a href=\"http:\/\/zlab.bu.edu\/~phaverty\/SupplementalData\/CisML\/\">CisML<\/a> An XML format for Sequence Motif Detection Programs<\/p>\n<p><a href=\"http:\/\/zlab.bu.edu\/~mfrith\/NucFreqMat.html\">Cis\u2010element info<\/a> Count matrices and background info for some \/cis\/\u2010elements<\/p>\n<p><a href=\"http:\/\/zlab.bu.edu\/ICSF\/\">ICSF<\/a> Identifies conserved structural features at sequentially degenerate locations in transcription factor binding sites<\/p>\n<p><a href=\"http:\/\/zlab.bu.edu\/~mfrith\/possum\/\">Possum<\/a> Simple matrix\u2010based motif search<\/p>\n<p><a href=\"http:\/\/biowulf.bu.edu\/zlab\/promoser\/\">Promoser<\/a> Human mouse and rat promoter extraction service<\/p>\n<p><a href=\"http:\/\/zlab.bu.edu\/repfind\/\">REPFIND<\/a> Find clustered, exact repeats in nucleotide sequences<\/p>\n<p><a href=\"http:\/\/zlab.bu.edu\/site2genome\/\">Site2genome<\/a> Locate sites in the human, mouse and rat genomes<\/p>\n<\/div>\n<div style=\"cursor: pointer;\" onclick=\"openClose('a2')\">\n<h2><a>DNA\/RNA Sequences<\/a><\/h2>\n<p>\u00a0<\/p>\n<\/div>\n<div id=\"a2\" class=\"texter\">\n<p><a href=\"http:\/\/zlab.bu.edu\/cluster-buster\/\">Cluster\u2010Buster<\/a> Program for finding clusters of pre\u2010specified motifs in nucleotide sequences<\/p>\n<p><a href=\"http:\/\/zlab.bu.edu\/~mfrith\/comet\/\">Comet<\/a> Cluster of Motifs E\u2010value Tool finds statistically significant clusters of motifs in a DNA sequence<\/p>\n<p><a href=\"http:\/\/zlab.bu.edu\/~mfrith\/cister.shtml\">Cister<\/a> Cister predicts regulatory regions in DNA sequences by searching for clusters of cis\u2010elements.<\/p>\n<p><a href=\"http:\/\/zlab.bu.edu\/clover\/\">Clover<\/a> Find overrepresented motifs in DNA sequences<\/p>\n<p><a href=\"http:\/\/tandem.bu.edu\/align.comp.tool.html\">CompAlign<\/a> Employs the mechanisms of string matching and string comparison yet avoids the overdependence of those methods on position\u2010by\u2010position matching<\/p>\n<p><a href=\"http:\/\/geneva.bu.edu\/faster.html\">FastER<\/a> Identification of genes with fast\u2010evolving regions in closely related genomes<\/p>\n<p><a href=\"http:\/\/genomics10.bu.edu\/terrence\/gems\/\">GEMS<\/a> Gene Expression Module Sampler biclustering based on a Gibbs sampling paradigm<\/p>\n<p><a href=\"http:\/\/zlab.bu.edu\/glam\/\">GLAM<\/a> Gapless Local Alignment of Multiple sequences: program for discovering functional motifs shared by a set of nucleotide sequences<\/p>\n<p><a href=\"http:\/\/biowulf.bu.edu\/MotifViz\/\">MotifViz<\/a> Integration of tools for detecting overrepresented motifs<\/p>\n<p><a href=\"http:\/\/genomics10.bu.edu\/yangsu\/rankgene\/\">RANKGENE<\/a> 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<\/p>\n<p><a href=\"http:\/\/zlab.bu.edu\/rover\/\">ROVER<\/a> Find relatively overrepresented motifs in DNA sequences<\/p>\n<p><a href=\"http:\/\/zlab.bu.edu\/SeqVISTA\/\">SeqVISTA<\/a> A viewer of sequences and their annotations; now with a Motif module for integrating transcriptional regulation analysis tools<\/p>\n<p><a href=\"http:\/\/genomics11.bu.edu\/Tractor\">Tractor<\/a> Program to computationally identify transcription factors with over\u2010represented binding sites in the upstream regions of co\u2010expressed human genes<\/p>\n<\/div>\n<div style=\"cursor: pointer;\" onclick=\"openClose('a3')\">\n<h2><a>Protein Engineering<\/a><\/h2>\n<p>\u00a0<\/p>\n<\/div>\n<div id=\"a3\" class=\"texter\">\n<p><a href=\"http:\/\/zlab.bu.edu\/k2\/\">K2<\/a> A genetic algorithm\u2010based protein structure alignment tool<\/p>\n<p><a href=\"http:\/\/biowulf.bu.edu\/FAST\/\">FAST<\/a> A newer protein structure alignment tool, based on graph theory<\/p>\n<p><a href=\"http:\/\/zlab.bu.edu\/SMM\/\">SMM<\/a> A matrix\u2010based algorithm for predicting peptides binding to Major Histocompatibility Complex<\/p>\n<p><a href=\"http:\/\/zdock.umassmed.edu\/software\/\">ZDOCK<\/a> Rigid\u2010body protein\u2010protein docking software, using a Fast Fourier Transform search algorithm<\/p>\n<p><a href=\"http:\/\/zdock.umassmed.edu\/software\/\">RDOCK<\/a> A refinement method to minimize energy and re\u2010rank ZDOCK predictions<\/p>\n<p><a href=\"http:\/\/zlab.umassmed.edu\/zdock\/benchmark\">Docking Benchmark<\/a> A large set of test cases for evaluating the performance of docking algorithms<\/p>\n<p><a href=\"http:\/\/zdock.umassmed.edu\/software\/\">ZDOCK Conv3D<\/a> ZDOCK optimized with a new convolution library, resulting in improved speed and less memory usage<\/p>\n<p><a href=\"http:\/\/zdock.umassmed.edu\/software\/\">ZDOCK Server<\/a> An automated server for running ZDOCK, with capabilities for blocking and filtering contact residues<\/p>\n<\/div>\n<div style=\"cursor: pointer;\" onclick=\"openClose('a4')\">\n<h2><a>Database Applications<\/a><\/h2>\n<p>\u00a0<\/p>\n<\/div>\n<div id=\"a4\" class=\"texter\">\n<p><a href=\"http:\/\/genomics10.bu.edu\/GeneChords\">GeneChords<\/a> Retrieve conserved gene cluster data from a number of microbial genomes as well as perform searches based on genomic context<\/p>\n<p><a href=\"http:\/\/geneva.bu.edu\/\">GENEVA<\/a> Catalogues SVGs (segmentally variable genes) in several complete microbial genomes.<\/p>\n<p><a href=\"http:\/\/zlab.bu.edu\/HugeSearch\">HuGE Index<\/a> Database of gene expression in normal human tissues<\/p>\n<p><a href=\"https:\/\/tandem.bu.edu\">Inverted Repeats Finder<\/a> Public repository of information on inverted repeats in genomic DNA<\/p>\n<p><a href=\"http:\/\/dna.bu.edu\/orchid\/\">ORChID<\/a> The \u2219OH Radical Cleavage Intensity Database (\u2219ORChID) stores hydroxyl radical cleavage data of DNA sequences<\/p>\n<p><a href=\"http:\/\/genomics10\/operons\/\">Operons<\/a> Functional Gene Clusters, Operons with applications to bacterial microarray analys, pathway reconstruction, functional annotation, and system biology based on graph matching<\/p>\n<p><a href=\"http:\/\/genomics10.bu.edu\/optimus\">Optimus<\/a> Retrieve conserved gene cluster data from a number of microbial genomes as well as perform searches based on genomic context<\/p>\n<p><a href=\"http:\/\/predictome.bu.edu\/\">Predictome<\/a> Tool for visualizing the predicted functional associations among genes and proteins in many different organisms<\/p>\n<p><a href=\"https:\/\/tandem.bu.edu\">Tandem Repeat Database<\/a> Public repository of information on tandem repeats in genomic DNA<\/p>\n<p><a href=\"http:\/\/visant.bu.edu\/\">VisANT<\/a> Web\u2010based software framework for visualizing and analyzing many types of networks of biological interactions and associations<\/p>\n<p><a href=\"http:\/\/visantst.bu.edu\/elisa\/\">ELISA<\/a> Evolutionary Lineage Inferred from Structural Alignment<\/p>\n<\/div>\n<div style=\"cursor: pointer;\" onclick=\"openClose('a5')\">\n<h2><a>Transcription Factor Binding Prediction Tools<\/a><\/h2>\n<p>\u00a0<\/p>\n<\/div>\n<div id=\"a5\" class=\"texter\">\n<p><a href=\"http:\/\/cagt10.bu.edu\/BSG\/\">BSG<\/a> Graphical Theoretical Prediction of Transcription Factor Binding Sites<\/p>\n<p><a href=\"http:\/\/cagt10.bu.edu\/SVMotif\/index.html\">SVMotif<\/a> A SVM Based Transcription Factor Binding Motif Finder<\/p>\n<p><a href=\"http:\/\/cagt10.bu.edu\/TFSVM\/\">TFSVM <\/a>Transcription Factor Binding Site Detection by Machine Learning<\/p>\n<\/div>\n<div style=\"cursor: pointer;\" onclick=\"openClose('a6')\">\n<h2><a>Cellular Metabolism<\/a><\/h2>\n<p>\u00a0<\/p>\n<\/div>\n<div id=\"a6\" class=\"texter\">\n<p><a href=\"http:\/\/ohmics.bu.edu\/\">OHMICS <\/a>Oral Human Microbiome Integrated Computational System<\/p>\n<\/div>\n","protected":false},"excerpt":{"rendered":"<p>Below you will find several categories of computational research tools, databases and applications developed by members of the BU Bioinformatics community. Gene Regulation \u00a0 Carrie Generate transcriptional regulatory networks from microarray and promoter sequence data CisML An XML format for Sequence Motif Detection Programs Cis\u2010element info Count matrices and background info for some \/cis\/\u2010elements ICSF [&hellip;]<\/p>\n","protected":false},"author":1443,"featured_media":0,"parent":0,"menu_order":51,"comment_status":"closed","ping_status":"closed","template":"","meta":[],"_links":{"self":[{"href":"https:\/\/www.bu.edu\/bioinformatics\/wp-json\/wp\/v2\/pages\/3585"}],"collection":[{"href":"https:\/\/www.bu.edu\/bioinformatics\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.bu.edu\/bioinformatics\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.bu.edu\/bioinformatics\/wp-json\/wp\/v2\/users\/1443"}],"replies":[{"embeddable":true,"href":"https:\/\/www.bu.edu\/bioinformatics\/wp-json\/wp\/v2\/comments?post=3585"}],"version-history":[{"count":50,"href":"https:\/\/www.bu.edu\/bioinformatics\/wp-json\/wp\/v2\/pages\/3585\/revisions"}],"predecessor-version":[{"id":3668,"href":"https:\/\/www.bu.edu\/bioinformatics\/wp-json\/wp\/v2\/pages\/3585\/revisions\/3668"}],"wp:attachment":[{"href":"https:\/\/www.bu.edu\/bioinformatics\/wp-json\/wp\/v2\/media?parent=3585"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}