Tools

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Below we highlight some of our tools and data sets. For an overview of the associated published literature, please visit [http://papers.gersteinlab.org/subject/tools/index.html our tools publication page]. You may also view a [http://papers.gersteinlab.org/subject/coretools/index.html list of the papers associated with our core tools]. Source code is available on our [http://github.com/gersteinlab lab Github page].
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Please refer to the [[Resources]] page.
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=Tool Portals=
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=== MolMovDB  ===
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:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
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!Name!!class="unsortable"|Description
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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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Servers and a suite of accessory tools for the analysis of conformational changes in protein and nucleic acid structures. 
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===Networks===
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:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
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!Name!!class="unsortable"|Description
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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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===Pseudogene.org===
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:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
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!Name!!class="unsortable"|Description
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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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===Structural Variants (SV)===
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:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
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!Name!!class="unsortable"|Description
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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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Software tools that may be used to investigate Structural Variations (SVs) and Copy Number Variations (CNVs).
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=Data Sets=
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:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
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!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;"|2009||This database, which is part of the PEMer package, contains information about structural variants and associated breakpoints.
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=Evolution=
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:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
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!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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=Genome Technology Tools=
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===Allele-Specific Effects===
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:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
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!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||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 maps RNA-seq and ChIP-seq functional genomic data onto this personal genome. Consequently, locations in which there are differences in number of mapped reads between maternally- and paternally-derived sequences can be identified, thereby providing evidence for allele-specific events.
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===ChiP-Seq ===
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:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
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!Name!!Release Date!!class="unsortable"|Description
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|style="width:15%; text-align:center;"|[http://www.gersteinlab.org/proj/PeakSeq/ '''PeakSeq'''] <br> [http://github.gersteinlab.org/PeakSeq/ Github repo] ||style="width:7%; 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.
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===Functional Annotation ===
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:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
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!Name!!Release Date!!class="unsortable"|Description
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|style="width:15%; text-align:center;"|[http://funseq.gersteinlab.org/ '''FunSeq''']||style="width:7%; text-align:center;"|2013||FunSeq can be used to automatically score and annotate the disease-causing potential of SNVs, particularly those which are non-coding. It can be used on cancer and personal genomes. Additionally, FunSeq can detect recurrent annotation elements in non-coding regions when running with multiple genomes. FunSeq is available for download.
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|style="width:15%; text-align:center;"|[http://vat.gersteinlab.org/ '''VAT'''] <br> [http://github.gersteinlab.org/vat/ Github repo] ||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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===Microarrays & Proteomics===
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|style="width:15%; text-align:center;"|[http://motips.gersteinlab.org/ '''MOTIPS''']||style="width:7%; text-align:center;"|2010||MOTIPS employs an efficient search algorithm to scan a target proteome for potential domain targets and to increase the accuracy of each hit by integrating a variety of pre-computed features, such as conservation, surface propensity, and disorder.
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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 (PARE) is 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 may warrant further investigation.
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===RNA-Seq===
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:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
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!Name!!Release Date!!class="unsortable"|Description
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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 efficient, multifaceted toolbox for analyzing continuous signal and discrete region tracks from high-throughput genomic experiments, such as RNA-seq or ChIP-chip signal profiles from the ENCODE and modENCODE projects, or lists of single nucleotide polymorphisms from the 1000 genomes project.
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|style="width:15%; text-align:center;"|[http://archive.gersteinlab.org/proj/rnaseq/fusionseq/ '''FusionSeq''']<br>[http://github.gersteinlab.org/FusionSeq/ Github repo]||style="width:7%; text-align:center;"|2010||FusionSeq may be used to identify fusion transcripts from paired-end RNA-sequencing. FusionSeq includes filters to remove spurious candidate fusions with artifacts, such as misalignment or random pairing of transcript fragments, and it ranks candidates according to several statistics. It also includes a module to identify exact sequences at breakpoint junctions.
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|style="text-align: center;"|[http://archive.gersteinlab.org/proj/rnaseq/IQSeq/ '''IQseq''']<br>[http://github.gersteinlab.org/IQSeq/ Github repo]||style="text-align:center;"|2012||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="text-align: center;"|[http://code.google.com/p/lesseq/ '''LESSeq''']<br>[http://github.gersteinlab.org/LESSeq/ Github repo]||style="text-align:center;"|2014||Local Event-based analysis of alternative Splicing using RNA-Seq
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|style="text-align: center;"|[http://archive.gersteinlab.org/proj/rnaseq/rseqtools/ '''RSEQtools''']<br>[http://github.gersteinlab.org/RSEQtools/ Github repo]||style="text-align:center;"|2011||A suite of tools that use Mapped Read Format (MRF) for the analysis of RNA-Seq experiments. MRF is a compact data 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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=== Structural Variation ===
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:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
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!Name!!Release Date!!class="unsortable"|Description
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|style="width:15%; text-align:center;"|[http://sv.gersteinlab.org/age/ '''AGE''']<br> [http://papers.gersteinlab.org/papers/age/index.html (citation)]||style="width:7%; text-align:center;"|2011|| AGE is used for defining breakpoints of genomic structural variants at single-nucleotide resolution, using optimal alignments with gap excision.
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|style="width:15%; text-align:center;"|[http://sv.gersteinlab.org/cnvnator/ '''CNVnator'''] <br>[http://papers.gersteinlab.org/papers/CNVnator/index.html (citation)]||style="width:7%; text-align:center;"|2011|| CNVnator may be used to discover, genotype, and characterize typical and atypical CNVs from familial and population genome sequencing.
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=Networks=
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!Name!!Release Date!!class="unsortable"|Description
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|style="width:15%; text-align:center;"|[http://archive.gersteinlab.org/proj/DynaSIN/index.html '''DynaSIN''']||style="width:7%; text-align:center;"|2011||The Dynamic Structure Interaction Network (DynaSIN) is a resource for studying protein-protein interaction networks in the context of conformational changes.
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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 on to networks, allowing for graphical visualization, textual navigation, and topological analysis. 
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|style="width:15%; text-align:center;"|[http://networks.gersteinlab.org/genome/interactions/networks/core.html '''TopNet''']||style="width:7%; text-align:center;"|2004||TopNet is an automated web tool designed compare the topologies of sub-networks, looking for global differences associated with different types of proteins. This automated web tool designed to address this question, calculating and comparing topological characteristics for different sub-networks derived from any given protein 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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=Structure and Macromolecular Motions=
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|style="width:15%; text-align:center;"|  [http://3vee.molmovdb.org/ '''3V''']||style="width:7%; text-align:center;"|2010||
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The 3V web server extracts and comprehensively analyzes the internal volumes of input RNA and protein structures. It identifies internal volumes by taking the difference between two rolling-probe solvent-excluded surfaces.
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|style="width:15%; text-align:center;"|[http://helix.gersteinlab.org/ '''HIT''']||style="width:7%; text-align:center;"|2006||The Helix Interaction Tool (HIT) is a comprehensive package for analyzing helix-helix packing in proteins. This enables the user to obtain quantitative measures of the helix interaction surface area and helix crossing angle, as well as several methods for visualizing the helical interaction.
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|style="width:15%; text-align:center;"|[http://geometry.molmovdb.org '''Macromolecular Geometry and 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 is a library functions for analyzing structures, a convenient interactive command-line interpreter, and software for the calculation of geometrical quantities associated with macromolecular structures and their motions.
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|style="width:15%; text-align:center;"|[http://www2.molmovdb.org/wiki/info/index.php/Morph_Server '''Morph Server''']||style="width:7%; text-align:center;"|2000||A web server for generating and viewing models of protein conformational change using interpolation with energy minimization. The user may opt to use either single- or multi-chain proteins as input.
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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 "https://info.gersteinlab.org/Tools"
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