Software
Many of the research methods developed by Center investigators are packaged into software applications and computational services which are made freely available to the scientific community:
| Software name | ADOMETA |
| Description | ADOMETA is a bioinformatics resource designed to predict genes for orphan metabolic activities - known biochemical activities not currently assigned to genes in some or all organisms. ADOMETA returns a ranked list of genes likely to catalyze a given metabolic activity in a selected organism. |
| URL to software page | http://vitkuplab.c2b2.columbia.edu/adometa/adometa.html |
| Lead investigator(s) | Dennis Vitkup |
| Software name | ARACNE |
| Description | ARACNE is an algorithm for inferring gene regulatory networks from a set of microarray experiments. The method uses mutual information to identify genes that are co-expressed and then applies the data processing inequality to filter out interactions that are likely to be indirect. |
| URL to software page | http://wiki.c2b2.columbia.edu/califanolab/index.php/Software |
| Lead investigator(s) | Andrea Califano |
| Software name | Biolearn 1.0 |
| Description | Biolearn is a general package for applying probabilistic graphical models to biological applications. Biolearn release 1.0 is concentrated on structure learning for bayesian networks; future releases are expected to include other types of graphical models, support inference applications, and allow plug-and-play addition of new types of probability distributions, scoring functions and search algorithms. |
| URL to software page | http://www.c2b2.columbia.edu/danapeerlab/html/biolearn.html |
| Lead investigator(s) | Dana Pe'er |
| Software name | B Cell Interactome |
| Description | The B cell interactome (BCI) is a network of protein-protein, protein-DNA and modulatory interactions in human B cells. The network contains known interactions (reported in public databases) and predicted interactions by a Bayesian evidence integration framework which integrates a variety of generic and context specific experimental clues about protein-protein and protein-DNA interactions - such as a large collection of B cell expression profiles - with inferences from different reverse engineering algorithms, such as GeneWays and ARACNE. Modulatory interactions are predicted by MINDY, an algorithm for the prediction of modulators of transcriptional interactions. |
| URL to software page | http://wiki.c2b2.columbia.edu/califanolab/index.php/Software |
| Lead investigator(s) | Andrea Califano |
| Software name | Camelot |
| Description | CAusal Modeling with Expression Linkage for cOmplex Traits (Camelot) provides a framework to both model complex traits and identify the potential underlying causal factors. Briefly, Camelot takes genotype, gene expression and phenotype data as input, and output a linear regression model that uses genotype and expression to predict phenotype. Powered by regularized linear regression, Camelot aims to choose features (either genotype or gene expression) that are predictive (and likely causal) to the phenotype. In addition, Camelot also provides functions to prioritize genes residing within a locus that is associated with the trait. |
| URL to software page | http://www.c2b2.columbia.edu/danapeerlab/html/camelot.html |
| Lead investigator(s) | Dana Pe'er |
| Software name | CLEANER |
| Description | R-system software package for the assembly of informative, transcript-specific probe-clusters for Affymetrix expression microarrays. |
| URL to software page | http://wiki.c2b2.columbia.edu/califanolab/index.php/Cleaner |
| Lead investigator(s) | Mariano Alvarez |
| Software name | CONDEX (condr) |
| Description | HMM Model to detect copy number variants in exome sequence data |
| URL to software page | http://code.google.com/p/condr/ |
| Lead investigator(s) | Itsik Pe'er |
| Software name | CONEXIC |
| Description | COpy Number and EXpression In Cancer (CONEXIC) is an algorithm that integrates matched copy number (amplifications and deletions) and gene expression data from tumor samples to identify driving mutations and the processes they influence. CONEXIC is inspired by Module Networks (Segal et al, 2003), but has been augmented by a number of critical modifications that make it suitable for identifying drivers. CONEXIC uses a score-guided search to identify the combination of modulators that best explains the behavior of a gene expression module across tumor samples and searches for those with the highest score within the amplified or deleted region. |
| URL to software page | http://www.c2b2.columbia.edu/danapeerlab/html/conexic.html |
| Lead investigator(s) | Dana Pe'er |
| Software name | cryoEM Refinement Tools |
| Description | Programs and protocols that can be used to refine atomic structures, either experimentally determined or computationally constructed, within cryo-electron microscopy (cryoEM) density maps of macromolecular complexes. |
| URL to software page | http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:cryoEM |
| Lead investigator(s) | Barry Honig |
| Software name | DASH |
| Description | DASH (DASH Associates Shared Haplotypes) is a tool for detecting association to clusters of IBD segments detected by Germline. It builds upon pairwise IBD shared segments to infer clusters of IBD individuals. |
| URL to software page | http://www1.cs.columbia.edu/~gusev/dash/ |
| Lead investigator(s) | Itsik Pe'er |
| Software name | DelPhi |
| Description | DelPhi provides numerical solutions to the Poisson-Boltzmann equation (both linear and nonlinear form) for molecules of arbitrary shape and charge distribution. The current version is fast (the best relaxation parameter is estimated at run time), accurate (calculation of the electrostatic free energy is less dependent on the resolution of the lattice) and can handle extremely high lattice dimensions. It also includes flexible features for assigning different dielectric constants to different regions of space and treating systems containing mixed salt solutions. |
| URL to software page | http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:DelPhi |
| Lead investigator(s) | Barry Honig |
| Software name | EDGI |
| Description | EDGI (Enhancer Detection using only Genomic Information) integrates a traditional motif-discovery algorithm SPLASH with a novel local permutation-clustering algorithm PromoClust in order to identify large regulatory elements (e.g. enhancers) as evolutionarily conserved, order-independent clusters of short conserved motifs. EDGI relies on the evolutionary conservation of the binding sites for regulating transcription factors, without requiring knowledge of these transcription factors or their binding sites. |
| URL to software page | http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:EDGI |
| Lead investigator(s) | Barry Honig |
| Software name | EVE |
| Description | EVE is a simulation framework for microbial populations in complex dynamic environments. |
| URL to software page | https://tavazoielab.c2b2.columbia.edu/EVE/ |
| Lead investigator(s) | Saeed Tavazoie |
| Software name | FASD |
| Description | Frequency Analysis of Sequence Data (FASD) |
| URL to software page | http://projects.dbmi.columbia.edu/fasd/index.php |
| Lead investigator(s) | Raul Rabadan |
| Software name | FIRE |
| Description | FIRE is a motif discovery and characterization program based on mutual information. |
| URL to software page | https://tavazoielab.c2b2.columbia.edu/FIRE/ |
| Lead investigator(s) | Saeed Tavazoie |
| Software name | FIRE-pro |
| Description | FIRE-pro is a motif discovery and characterization program for proteins based on mutual information. |
| URL to software page | https://tavazoielab.c2b2.columbia.edu/FIRE-pro/ |
| Lead investigator(s) | Saeed Tavazoie |
| Software name | Genatomy |
| Description | Genatomy is a visualizing tool for biological data, such as gene expression, genotypes, growth curves, copy number variation and more. It can be used to analyze the data mathematically and to study the biological aspects of the data and the results. |
| URL to software page | http://www.c2b2.columbia.edu/danapeerlab/html/genatomy.html |
| Lead investigator(s) | Dana Pe'er |
| Software name | Germline |
| Description | GERMLINE is an algorithm for discovering long shared segments of Identity by Descent (IBD) between pairs of (unrelated) individuals in a large population. |
| URL to software page | http://www1.cs.columbia.edu/~gusev/germline/ |
| Lead investigator(s) | Itsik Pe'er |
| Software name | geWorkbench |
| Description | geWorkbench is a Java application that provides users with an integrated suite of genomics tools. It is built on an open-source, extensible architecture that promotes interoperability and simplifies the development of new as well as the incorporation of pre-existing components. The resulting system provides seamless access to a multitude of both local and remote data and computational services through an integrated environment that offers a unified user experience. Over 50 data analysis and visualization components have been developed for the framework, covering a wide range of genomics domains including gene expression, sequence, structure and network data. |
| URL to software page | http://www.geworkbench.org |
| Lead investigator(s) | Aris Floratos |
| Software name | GRASP |
| Description | A molecular visualization and analysis program. It is particularly useful for the display and manipulation of the surfaces of molecules and their electrostatic properties. |
| URL to software page | http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:GRASP |
| Lead investigator(s) | Anthony Nicholls, Barry Honig |
| Software name | GRASP2 |
| Description | GRASP2 is an updated version of the GRASP program used for macromolecular structure and surface visualization, contains a large number of new features and scientific tools: Enhanced GUI; Structure alignment and domain database scanning; A gaussian surface generator and new surface coloring schemes; Sequence visualization and alignment; Completed work can be stored in project files; Among the many objects that can be stored in a project file are views of the structure; defined subsets, surfaces; Direct printing to printers at full printer resolution. |
| URL to software page | http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:GRASP2 |
| Lead investigator(s) | Donald Petrey and Barry Honig |
| Software name | HADiT |
| Description | HADiT (Haplotype Amplification Distortion in Tumors) is a tool for computing and visualizing allelic distortion in tumor SNP data. Implements the Amplification Distortion Test (ADT). |
| URL to software page | http://www.cs.columbia.edu/~itsik/HADiT/HADiT.html |
| Lead investigator(s) | Itsik Pe'er |
| Software name | HATS |
| Description | HATS is a tool for calling the amplified alleles and constructing the amplified haplotype within called tumor amplicons. |
| URL to software page | http://www.cs.columbia.edu/~itsik/HATS/HATS.html |
| Lead investigator(s) | Itsik Pe'er |
| Software name | HLAIBD |
| Description | The Human Leukocyte Antigen (HLA) genes play a major role in adaptive immune response and are used to differentiate self cells from non-self cells. HLA genes are hyper variable with nearly every locus containing over a dozen alleles. This variation plays an important role in autoimmune disease and organ transplantation. HLA typing by serological methods is time consuming and expensive. HLABID is a new computational method to infer per-locus HLA types using shared segments Identical By Descent (IBD), inferred from genotype data. |
| URL to software page | http://www.cs.columbia.edu/~itsik/hla_ibd/index.html |
| Lead investigator(s) | Itsik Pe'er |
| Software name | Inference of Modules associated to eQTLs |
| Description | A tool for constructing modules regulated by eQTLs using gene expression and SNP variation data across multiple individuals. |
| URL to software page | http://www.cs.columbia.edu/~itsik/IMR_eQTL2/ |
| Lead investigator(s) | Itsik Pe'er |
| Software name | INFOSTIP |
| Description | A tool for selecting INdividual FOr Sequencing by Total Information Potential, based on GERMLINE output. |
| URL to software page | http://www.cs.columbia.edu/~itsik/INFOSTIP/readme.html |
| Lead investigator(s) | Itsik Pe'er |
| Software name | iPAGE |
| Description | iPAGE a functional and categorical enrichment program based on mutual information. |
| URL to software page | https://tavazoielab.c2b2.columbia.edu/iPAGE/ |
| Lead investigator(s) | Saeed Tavazoie |
| Software name | JACKAL |
| Description | Jackal is a collection of programs designed for the modeling and analysis of protein structures. Its core program is a versatile homology modeling package nest. JACKAL has the following capabilities: 1) comparative modeling based on single, composite or multiple templates; 2) side-chain prediction; 3) modeling residue mutation, insertion or deletion; 4) loop prediction; 5) structure refinement; 6) reconstruction of protein missing atoms;7) reconstruction of protein missing residues; 8) prediction of hydrogen atoms; 9) fast calculation of solvent accessible surface area; 10) structure superimposition. |
| URL to software page | http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:Jackal |
| Lead investigator(s) | Z. Xiang and B. Honig |
| Software name | JISTIC |
| Description | JISTIC is a tool for analyzing datasets of genome-wide copy number variation to identify driver aberrations in cancer. JISTIC is an improvement over the widely used GISTIC algorithm. |
| URL to software page | http://www.c2b2.columbia.edu/danapeerlab/html/jistic.html |
| Lead investigator(s) | Dana Pe'er |
| Software name | LitVAn |
| Description | Literature Vector Analysis, is an algorithm that searches forover-represented terms in papers associated with genes in a gene set. LitVAn uses a manually curated database (NCBI Gene) to connect genes with terms from the complete text of more than 70,000 published scientific articles. |
| URL to software page | http://litvan.bio.columbia.edu/ |
| Lead investigator(s) | Dana Pe'er |
| Software name | Mark-Us |
| Description | Mark-Us is a web server to assist the assessment of the biochemical function for a given protein structure. Mark-Us identifies related protein structures and sequences, detects protein cavities, and calculates the surface electrostatic potentials and amino acid conservation profile. The results can be browsed by an interactive web interface that allows to integrate Gene Ontology terms, UniProt features, and the Enzyme Classification. |
| URL to software page | http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:Mark-Us |
| Lead investigator(s) | Barry Honig |
| Software name | MatrixREDUCE |
| Description | Regulation of gene expression by a transcription factor requires physical interaction between the factor and the DNA, which can be described by astatistical mechanical model. Based on this model, the MatrixREDUCE algorithm uses genome-wide occupancy data for a transcription factor (e.g.ChIP-chip or mRNA expression data) and associated nucleotide sequences to discover the sequence-specific binding affinity of the transcription factor. The sequence specificity of the transcription factor's DNA-binding domain is modeled using a position-specific affinity matrix (PSAM), representing the change in the binding affinity (Kd) whenever a specific position within a reference binding sequence is mutated. The PSAM can be transformed into affinity logo for visualization using the utility program AffinityLogo, and a MatrixREDUCE run can be summarized in an easy-to-navigate webpage using HTMLSummary. |
| URL to software page | http://www.bussemakerlab.org/software/MatrixREDUCE |
| Lead investigator(s) | Harmen J. Bussemaker |
| Software name | MEDUSA and Gorgon |
| Description | MEDUSA is an algorithm for learning predictive models of transcriptional gene regulation from gene expression and promoter sequence data. By using a statistical learning approach based on boosting, MEDUSA learns cis regulatory motifs, condition-specific regulators, and regulatory programs that predict the differential expression of target genes. The regulatory program is specified as an alternating decision tree (ADT). The Java implementation of MEDUSA allows a number of visualizations of the regulatory program and other inferred regulatory information, implemented in the accompanying Gorgon tool, including hits of significant and condition-specific motifs along the promoter sequences of target genes and regulatory network figures viewable in Cytoscape. |
| URL to software page | http://cbio.mskcc.org/leslielab/software/medusa |
| Lead investigator(s) | David Quigley, Manuel Middendorf, Steve Lianoglou, Anshul Kundaje, Yoav Freund, Chris Wiggins, Christina Leslie |
| Software name | MINDY |
| Description | Given a transcription factor of interest, MINDY uses a large set of gene expression profile data to identify potential post-transcriptional modulators of the transcription factor's activity. MINDY is based on a three-way statistical interaction model that captures the post-transcriptional regulatory event where the ability of a transcription factor to activate/repress its target genes is monotonically controlled by a potential modulator gene. |
| URL to software page | http://wiki.c2b2.columbia.edu/califanolab/index.php/Software |
| Lead investigator(s) | Andrea Califano |
| Software name | Model Quality Assessment: Global and Local Quality Assessment of Protein Models |
| Description | Three protocols have been implemented for model quality assessment (MQA), including direct assessment of local qualities using statistical potentials and two machine-learning based protocols. The statistical potentials used here include newly developed solvation potentials, environmental potentials, pairwise potentials, hydrogen bonding potentials and backbone dihedral potentials. The normalized version of these potentials can be directly used to evaluate local qualities by plotting against residue numbers. |
| URL to software page | http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software |
| Lead investigator(s) | Barry Honig |
| Software name | MutaGeneSys |
| Description | MutaGeneSys uses genome-wide genotype data to estimate individual disease susceptibility. It integrates OMIM and HapMap-based single- and multi-marker predictors of causal SNPs to report the collection of associated alleles in a whole-genome-typed individual. |
| URL to software page | http://www1.cs.columbia.edu/~jds1/MutaGeneSys/ |
| Lead investigator(s) | Itsik Pe'er |
| Software name | Nest |
| Description | Modeling protein structure based on a sequence-template alignment. The current server works only for modeling with a single template. Part of jackal, which can be downloaded. |
| URL to software page | http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:nest |
| Lead investigator(s) | Xiang, Z. and Honig, B. |
| Software name | Opera |
| Description | OPERA is a tool for power estimation and design of whole-genome resequencing projects aimed at rare variant associations. |
| URL to software page | http://www.cs.columbia.edu/~itsik/OPERA/ |
| Lead investigator(s) | Itsik Pe'er |
| Software name | PoolDesign |
| Description | PoolDesign is a tool for designing overlapping pools for variant-carrier identification. |
| URL to software page | http://www.cs.columbia.edu/~itsik/Pooling/pooldesign.jar |
| Lead investigator(s) | Itsik Pe'er |
| Software name | PredUs |
| Description | PredUs (Prediction of Protein Interfaces Using Structural Alignment) is a tool to predict protein-protein interface based on interface conservation among structurally similar protein neighbors. |
| URL to software page | http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:PredUs |
| Lead investigator(s) | Barry Honig |
| Software name | PREPPI |
| Description | PREPPI is a database of predicted and experimentally determined protein-protein interactions (PPIs) for yeast and human. Predicted interactions are assigned a likelihood using a Bayesian framework that combines structural, functional, evolutionary and expression information. The database contains ~2 million predictions including 31,402 for yeast and 317,813 for human that are considered high confidence based on our analysis. Experimentally determined interactions are compiled from a set of public databases (e.g., DIP, IntAct, HPRD, etc). |
| URL to software page | http://bhapp.c2b2.columbia.edu/PREPPI/ |
| Lead investigator(s) | Barry Honig |
| Software name | PrISM |
| Description | PrISM is an integrated computational system where computational tools are implemented for protein sequence and structure analysis and modeling. |
| URL to software page | http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:PrISM |
| Lead investigator(s) | Barry Honig |
| Software name | Protein-DNA interface alignment |
| Description | The protein-DNA alignment software allows one to align the interfacial amino acids from two protein-DNA complexes based on the geometric relationship of each amino acid to its local DNA. |
| URL to software page | http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:Protein-DNA_Interface_Alignment |
| Lead investigator(s) | Barry Honig |
| Software name | Protein-DNA Modeling Interface Software |
| Description | The program can be used predict the conformation of the sidechains within a protein-DNA binding interface. |
| URL to software page | http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:Protein-DNA_Modeling_Interface |
| Lead investigator(s) | Barry Honig |
| Software name | REDUCE Suite |
| Description | The REDUCE Suite is a set of software tools to model the regulation of gene expression by transcription factors (TF). By directly correlating genome-wide mRNA expression or TF binding data (e.g. ChIP-chip) with associated nucleotide sequences, the REDUCE Suite can discover the sequence-specific binding affinity of a TF from a single experiment, using all measurements simultaneously, and without using any "background" sequence model. The REDUCE suite has its origin in the REDUCE algorithm of Bussemaker, Li, and Siggia, Nature Genetics (2001), which pioneered the use of motif-based linear regression model to discover cis-regulatory elements (motifs) and infer condition-specific transcription factor activities from a single genomewide mRNA expression profile. |
| URL to software page | http://bussemaker.bio.columbia.edu/software/REDUCE/ |
| Lead investigator(s) | Harmen Bussemaker |
| Software name | SCREEN |
| Description | A web server tool for identifying protein cavities and computing cavity attributes that can be applied for classification and analysis. |
| URL to software page | http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:SCREEN |
| Lead investigator(s) | Barry Honig |
| Software name | ShareViz |
| Description | Shareviz is a tool for graphical visualization of hidden relatedness based on GERMLINE output. |
| URL to software page | http://www.cs.columbia.edu/~itsik/sharevizWeb/shareviz.html |
| Lead investigator(s) | Itsik Pe'er |
| Software name | SIXPAC |
| Description | SIXPAC (Search for Interactions is Probably Approximately Complete) is an efficient, scalable search algorithm that finds synergy between pairs of physically unlinked SNPs (genome-wide) in large case-control datasets. |
| URL to software page | http://www.cs.columbia.edu/~snehitp/sixpac/ |
| Lead investigator(s) | Itsik Pe'er |
| Software name | SPLASH |
| Description | SPLASH (Structural Pattern Localization Analysis by Sequential Histograms) is a deterministic pattern discovery algorithm which can find sparse amino or nucleic acid patterns matching identically or similarly in a set of protein or DNA sequences. Sparse patterns of any length, up to the size of the input sequence can be discovered without significant loss in performance. Splash performance is extremely efficient. |
| URL to software page | http://amdec-bioinfo.cu-genome.org/html/Splash.html |
| Lead investigator(s) | Andrea Califano |
| Software name | STING Millennium |
| Description | A web based suite of programs for comprehensive and simultaneous analysis of structure and sequence: nature and volume of atomic contacts of both intra- and inter- chain types, analysis of the quality of structure, residue conservation and its relationship with intra-chain contacts, functional parameters are also deciphered. |
| URL to software page | http://luna.bioc.columbia.edu/SMS/STINGm/ |
| Lead investigator(s) | Barry Honig |
| Software name | String kernel package |
| Description | The string kernel package contains implementations for the mismatch and profile string kernels for use with support vector machine (SVM) classifiers for protein sequence classification. Both kernels compute similarity between protein sequences based on common occurrences of k-length subsequences (k-mers) counted with substitutions. Kernel functions for protein sequence data enable the training of SVMs for a range of prediction problems, in particular protein structural class prediction and remote homology detection. A version of the Spider MATLAB machine learning package is also bundled with the code, which allows users to train SVMs and evaluate performance on test sets with the packaged software. |
| URL to software page | http://svm-fold.c2b2.columbia.edu/ |
| Lead investigator(s) | Christina Leslie |
| Software name | SURFace |
| Description | SURFace algorithms are programs that calculate solvent accessible surface area and curvature corrected solvent accessible surface area |
| URL to software page | http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:SURFace_Algorithms |
| Lead investigator(s) | Barry Honig |
| Software name | T-profiler |
| Description | T-profiler is a web-based tool that uses the t-test to score changes in the average activity of pre-defined groups of genes. The gene groups are defined based on Gene Ontology categorization, ChIP-chip experiments, upstream matches to a consensus transcription factor binding motif, and location on the same chromosome, respectively. If desired, an iterative procedure can be used to select a single, optimal representative from sets of overlapping gene groups. A jack-knife procedure is used to make calculations more robust against outliers. T-profiler makes it possible to interpret microarray data in a way that is both intuitive and statistically rigorous, without the need to combine experiments or choose parameters. |
| URL to software page | http://www.t-profiler.org |
| Lead investigator(s) | Harmen J. Bussemaker |
| Software name | Target Explorer |
| Description | Automated process of prediction of complex regulatory elements for specified set of transcription factors in Drosophila melanogaster genome. Target Explorer is a complex tool with user-friendly self-explanatory Web-interface that allows to user: 1. create customized library of TF binding site matrices based on user defined sets of training sequences; 2. search for new clusters of binding sites for specified set of TFs; 3.extract annotation for potential target genes. |
| URL to software page | http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:Target_Explorer |
| Lead investigator(s) | Barry Honig and Richard Mann |
| Software name | TEISER |
| Description | TEISER is a de-novo motif discovery tool for finding informative structural elements in RNA. |
| URL to software page | https://tavazoielab.c2b2.columbia.edu/TEISER/ |
| Lead investigator(s) | Saeed Tavazoie |
| Software name | TranscriptionDetector |
| Description | A tool for finding probes measuring significantly expressed loci in a genomic array experiment. Given expression data from some tiling array experiment, TranscriptionDetector decides the likelihood that a probe is detecting transcription from the locus in which it resides. Probabilities are assigned by making use of a background signal intensity distribution from a set of negative control probes. This tool is useful for the functional annotation of genomes as it allows for the discovery of novel transcriptional units independently of any genomic annotation. |
| URL to software page | http://www.bussemakerlab.org/software/TranscriptionDetector/ |
| Lead investigator(s) | Harmen J. Bussemaker |
| Software name | TransfactomeDB |
| Description | Accurate and comprehensive information about the nucleotide sequence specificity of trans-acting factors (TFs) is essential for computational and experimental analyses of gene regulatory networks. The Yeast Transfactome Database is a repository of sequence specificity models and condition-specific regulatory activities for a large number of DNA- and RNA-binding proteins in Saccharomyces cerevisiae. The sequence specificities in TransfactomeDB, represented as position-specific affinity matrices (PSAMs), are directly estimated from genomewide measurements of TF-binding using our previously published MatrixREDUCE algorithm, which is based on a biophysical model. For each mRNA expression profile in the NCBI Gene Expression Omnibus, we used sequence-based regression analysis to estimate the post-translational regulatory activity of each TF for which a PSAM is available. The trans-factor activity profiles across multiple experiments available in TransfactomeDB allow the user to explore potential regulatory roles of hundreds of TFs in any of thousands of microarray experiments. |
| URL to software page | http://bussemaker.bio.columbia.edu:8080/YeastTransfactomeDB/ |
| Lead investigator(s) | Harmen Bussemaker |
| Software name | VISTAL |
| Description | A two-dimensional visualization tool for structural alignments. VISTAL describes structures as a series of secondary structure elements, and places matched residues one on top of each other colored according to the three-dimensional distance of their Ca atoms. |
| URL to software page | http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:Vistal |
| Lead investigator(s) | Barry Honig |
| Software name | Xplorigin |
| Description | A tool for parsing population ancestry of admixed individuals. |
| URL to software page | http://www.cs.columbia.edu/~itsik/Xplorigin/Xplorigin.htm |
| Lead investigator(s) | Itsik Pe'er |
| Software name | Zinfandel |
| Description | Zinfandel is a tool for detecting CNVs from low-pass WGS data. |
| URL to software page | http://www.cs.columbia.edu/~itsik/zinfandel/ |
| Lead investigator(s) | Itsik Pe'er |