Tools

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Below we highlight some of our tools and data sets. For an overview of tool-centric lab publications see our [http://papers.gersteinlab.org/subject/tools tools papers page]. The source code of many of our tools in available on our [http://github.gersteinlab.org lab Github page].
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Please refer to the [[Resources]] page.
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=Tools portals=
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=== MolMovDB  ===
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:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
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|- bgcolor="lightsteelblue"
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!Tool Name!!class="unsortable"|Description
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|-style="height: 100px;"
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|style="width:15%; text-align:center;"| [[File:Morph-icon.jpg‎]] <br> [http://molmovdb.mbb.yale.edu/molmovdb/ MolMovDB] ||
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This describes the motions that occur in proteins and other macromolecules, particularly using movies. Associated with it are a variety of free software tools and servers for structural analysis. 
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===Pseudogene.org===
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:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
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|- bgcolor="lightsteelblue"
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!Tool Name!!class="unsortable"|Description
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|-style="height: 100px;"
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|style="width:15%; text-align:center;"| [[File:pseudogene.png‎]] <br> [http://www.pseudogene.org/ Pseudogene.org]] ||Pseudogene.org is a collection of resources related to our efforts to survey eukaryotic genomes for pseudogene sequences, "pseudo-fold" usage, amino-acid composition, and single-nucleotide polymorphisms (SNPs) to help elucidate the relationships between pseudogene families across several organisms.
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===Networks===
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:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
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|- bgcolor="lightsteelblue"
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!Tool Name!!class="unsortable"|Description
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|-style="height: 10px;"
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|style="width:15%; text-align:center;"| [[File:Network.jpg|center|x75px]] <br> [http://networks.gersteinlab.org/ Networks] ||
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The Gerstein lab has been a pioneer in applying network analysis to generate knowledge form large-scale experiments.To this end, we have developed a portal for our network research.
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===Structural Variants (SV)===
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:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
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|- bgcolor="lightsteelblue"
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!Tool Name!!class="unsortable"|Description
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|-style="height: 100px;"
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|style="width:15%; text-align:center;"| [[File:SVpage logo.png‎|center|x85px]] <br> [http://sv.gersteinlab.org/ Structural Variants]||
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Structural Variations (SVs) and Copy Number Variations (CNVs) are a major source of genetic variation. our analysis tools are available in this portal.
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=Genome Technology Tools=
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===WGS ===
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:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
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|- bgcolor="lightsteelblue"
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!Tool Name!!Release Date!!class="unsortable"|Description
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|-style="height: 100px;"
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|style="width:15%; text-align:center;"|[http://funseq.gersteinlab.org/ '''FunSeq''']||style="width:7%; text-align:center;"|2013|| This site can be used to automatically score and annotate disease-causing potential of SNVs, particularly the non-coding ones. It can be used on cancer and personal genomes. It also contains a downloadable tool.
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===Exome ===
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:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
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!Tool Name!!Release Date!!class="unsortable"|Description
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|-style="height: 100px;"
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|style="width:15%; text-align:center;"|[http://sv.gersteinlab.org/cnvnator/ '''CNVnator''']||style="width:7%; text-align:center;"|2013|| An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing.
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|-style="height: 100px;"
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|style="width:15%; text-align:center;"|[http://sv.gersteinlab.org/age/ '''AGE''']||style="width:7%; text-align:center;"|2013|| AGE: defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision.
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===Functional Annotation ===
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:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
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!Tool Name!!Release Date!!class="unsortable"|Description
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|-style="height: 100px;"
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|style="width:15%; text-align:center;"|[http://vat.gersteinlab.org/ '''VAT''']||style="width:7%; text-align:center;"|2012|| A computational framework to functionally annotate variants in personal genomes using a cloud-computing environment.
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===RNA-seq===
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:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
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!Tool Name!!Release Date!!class="unsortable"|Description
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|-style="height: 100px;"
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|style="width:15%; text-align:center;"|[http://archive.gersteinlab.org/proj/rnaseq/fusionseq/ '''FusionSeq''']<br>[http://github.com/gersteinlab/FusionSeq Github repo]||style="width:7%; text-align:center;"|2011||FusionSeq: a modular framework for finding gene fusions by analyzing Paired-End RNA-Sequencing data.
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|-style="height: 100px;"
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|style="width:15%; text-align:center;"|[http://act.gersteinlab.org/ '''ACT''']||style="width:7%; text-align:center;"|2011||The aggregation and correlation toolbox (ACT) is an aggregation and correlation toolbox for analyses of genome tracks.
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|-style="height: 100px;"
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|style="text-align: center;"|[http://archive.gersteinlab.org/proj/rnaseq/fusionseq/ '''FusionSeq''']||style="width:7%; text-align:center;"|2003||A computational framework for detecting chimeric transcripts from paired-end RNA-seq experiments. It includes filters to remove spurious candidate fusions with artifacts, such as misalignment or random pairing of transcript fragments, and provides a ranked list of fusion-transcript candidates that can be further evaluated via experimental methods. FusionSeq also contains a module to identify exact sequences at breakpoint junctions.
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|-style="height: 100px;"
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|style="text-align: center;"|[http://archive.gersteinlab.org/proj/rnaseq/IQSeq/ '''IQseq''']||style="text-align:center;"|2010||A tool for isoform quantification with RNA-seq data. Given isoform annotation and alignment of RNA-seq reads, it will use an EM algorithm to infer the most probable expression level for each isoform of a gene.
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|-style="height: 100px;"
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|style="text-align: center;"|[http://archive.gersteinlab.org/proj/rnaseq/rseqtools/ '''RSEQtools''']||style="text-align:center;"|2010||A suite of tools that use Mapped Read Format (MRF) for the analysis of RNA-Seq experiments.  MRF was developed to address privacy concerns associated with the potential for mRNA sequence reads to identify and genetically characterise specific individuals; it is a compact data summary format that enables anonymization of confidential sequence information, while maintaining the ability to conduct subsequent functional genomics studies.  RSEQtools provides a suite of modules that convert to/from MRF data and perform common tasks such as calculating gene expression values, generating signal tracks of mapped reads, and segmenting that signal into actively transcribed regions.
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===ChIP===
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:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
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!Tool Name!!Release Date!!class="unsortable"|Description
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|-style="height: 100px;"
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|style="width:15%; text-align:center;"|[http://www.gersteinlab.org/proj/BoCaTFBS/ '''BoCaTFBS''']||style="width:7%; text-align:center;"|2006||A boosted cascade learner to refine the binding sites suggested by ChIP-chip experiments. This tool is based on a data mining approach combining noisy data from ChIP-chip experiments with known binding site patterns. BoCaTFBS uses boosted cascades of classifiers for optimum efficiency, in which components are alternating decision trees; it exploits interpositional correlations; and it explicitly integrates massive negative information from ChIP-chip experiments.
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|-style="height: 100px;"
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|style="text-align: center;"|[http://www.gersteinlab.org/proj/PeakSeq/ '''PeakSeq''']||style="text-align:center;"|2009||A tool for calling peaks corresponding to transcription factor binding sites from ChIP-Seq data scored against a matched control such as Input DNA.  PeakSeq employs a two-pass strategy in which putative binding sites are first identified in order to compensate for genomic variation in the 'mappability' of sequences, before a second pass filters out sites not significantly enriched compared to the normalized control, computing precise enrichments and significances.  Our scoring procedure enables us to optimize experimental design by estimating the depth of sequencing required for a desired level of coverage and demonstrating that more than two replicates provides only a marginal gain in information.
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===Allele-specific effects===
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:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
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!Tool Name!!Release Date!!class="unsortable"|Description
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|style="width:15%; text-align:center;"|[http://alleleseq.gersteinlab.org/home.html '''AlleleSeq''']||style="width:7%; text-align:center;"|2011||The AlleleSeq is a computational pipeline that is used to study allele-specific expression (ASE) and allele specific binding (ASB). The pipeline first constructs a diploid personal genome sequence, then map RNA-seq and ChIP-seq functional genomic data onto this personal genome. Consequently, locations where there are differences in number of mapped reads between maternally- and paternally-derived sequences can be identified and these provide evidence for allele-specific events.
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===Microarrays & Proteomics===
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:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
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!Tool Name!!Release Date!!class="unsortable"|Description
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|style="width:15%; text-align:center;"|[http://motips.gersteinlab.org/ '''motips''']||style="width:7%; text-align:center;"|2003||MOTIPS: Automated Motif Analysis for Predicting Targets of Modular Protein Domains.
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|-style="height: 100px;"
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|style="width:15%; text-align:center;"|[http://bioinfo.mbb.yale.edu/ExpressYourself '''ExpressYourself''']||style="width:7%; text-align:center;"|2003||An interactive platform for background correction, normalization, scoring, and quality assessment of raw microarray data.
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|-style="height: 100px;"
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|style="width:15%; text-align:center;"|[http://proteomics.gersteinlab.org '''PARE''']||style="width:7%; text-align:center;"|2007||(Protein Abundance and mRNA Expression). A tool for comparing protein abundance and mRNA expression data.  In addition to globally comparing the quantities of protein and mRNA, PARE allows users to select subsets of proteins for focused study (based on functional categories and complexes). Furthermore, it highlights correlation outliers, which are potentially worth further examination.
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|-style="height: 100px;"
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|style="width:15%; text-align:center;"|  [http://3vee.molmovdb.org/ 3vee]||style="width:7%; text-align:center;"|1998||
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3vee is collection of program for the assessment of volumes in protein files.
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|-style="height: 100px;"
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|style="width:15%; text-align:center;"| [http://geometry.molmovdb.org/ geometry]||style="width:7%; text-align:center;"|1999||
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calculation of geometrical quantities associated with macromolecular structures and their motions
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===Clustering===
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:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
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!Tool Name!!Release Date!!class="unsortable"|Description
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|style="width:15%; text-align:center;"|[http://bioinfo.mbb.yale.edu/expression/cluster '''Local Clustering''']||style="width:7%; text-align:center;"|2001||A new algorithm for local clustering to find timeshifted and/or inverted relationships in gene expression data is available as C source code.
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=Network Tools=
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:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
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!Tool Name!!Release Date!!class="unsortable"|Description
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|style="width:15%; text-align:center;"|[http://networks.gersteinlab.org/genome/interactions/networks/ '''TopNet''']||style="width:7%; text-align:center;"|2004||An automated web tool designed to calculate topological parameters and compare different sub-networks for any given network.
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|style="width:15%; text-align:center;"|[http://tyna.gersteinlab.org/tyna/ '''tYNA''']||style="width:7%; text-align:center;"|2006||(TopNet-like Yale Network Analyzer). A Web system for managing, comparing and mining multiple networks, both directed and undirected. tYNA efficiently implements methods that have proven useful in network analysis, including identifying defective cliques, finding small network motifs (such as feed-forward loops), calculating global statistics (such as the clustering coefficient and eccentricity), and identifying hubs and bottlenecks etc.
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=Evolution Tools=
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:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
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!Tool Name!!Release Date!!class="unsortable"|Description
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|style="width:15%; text-align:center;"|[http://coevolution.gersteinlab.org/coevolution/ '''Coevolution analysis of protein residues''']||style="width:7%; text-align:center;"|2008||An integrated online system that enables comparative analyses of residue coevolution with a comprehensive set of commonly used scoring functions, including Statistical Coupling Analysis (SCA), Explicit Likelihood of Subset Variation (ELSC), mutual information and correlation-based methods.
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=Structural Biology Tools=
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:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
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!Tool Name!!Release Date!!class="unsortable"|Description
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|style="width:15%; text-align:center;"|[http://spine.nesg.org '''SPINE''']||style="width:7%; text-align:center;"|2001||A laboratory-information management system (LIMS) for the [http://www.nesg.org NorthEast Structural Genomics Consortium]. The online version is restricted to consortium users, but most of the code is freely available for download.
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|-style="height: 100px;"
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|style="width:15%; text-align:center;"|[http://geometry.molmovdb.org '''Macromolecular Packing Tools''']||style="width:7%; text-align:center;"|1994-2009||A number of programs for calculating properties of protein and nucleic acid structures have been collected into a single distribution.  Included are a library of utility functions for dealing with structures, and a convenient interactive command-line interpreter.
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|style="width:15%; text-align:center;"|[http://helix.gersteinlab.org/ '''HIT''']||style="width:7%; text-align:center;"|2006||(Helix Interaction Tool). A web-based comprehensive package of tools for analyzing helix-helix interactions in proteins.
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==Data sets==
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:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
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!Tool Name!!Release Date!!class="unsortable"|Description
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|style="width:15%; text-align:center;"|[http://sv.gersteinlab.org/breakdb/ BreakDB]||style="width:7%; text-align:center;"|2008||This database, which is part of the PEMer package, contains information about structural variants and associated breakpoints.
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=Other=
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:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
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!Tool Name!!Release Date!!class="unsortable"|Description
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|style="width:15%; text-align:center;"|[http://pubnet.gersteinlab.org/ '''PubNet''']||style="width:7%; text-align:center;"|2005||A web-based tool that extracts several types of relationships returned by PubMed queries and maps them into networks, allowing for graphical visualization, textual navigation, and topological analysis. 
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|style="width:15%; text-align:center;"|[http://hub.gersteinlab.org/ir-supp/ '''HUB''']||style="width:7%; text-align:center;"|2001||A tool for leveraging the structure of the semantic web to enhance information retrieval for proteomics. This tool helps Proteomics researchers to be able to quickly retrieve relevant information from the web and the biomedical literature.
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==more tools==
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[[more tools]]
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Latest revision as of 14:50, 5 May 2014

Please refer to the Resources page.

Retrieved from "http://info.gersteinlab.org/Tools"
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