Tools

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[http://papers.gersteinlab.org/subject/tools Overview] of Lab Tools and Associated Publications
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=Pseudogene Tools=
=Pseudogene Tools=
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Revision as of 00:32, 7 November 2013

Overview of Lab Tools and Associated Publications

Contents

Pseudogene Tools

Tool NameRelease DateDescription
Pseudogene.org2001-2011A 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.


Genome Technology Tools

RNA-seq

Tool NameRelease DateDescription
ACT2011The aggregation and correlation toolbox (ACT) is an aggregation and correlation toolbox for analyses of genome tracks.
FusionSeq2010A 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.
IQseq2010A 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.
RSEQtools2010A 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.


ChIP

Tool NameRelease DateDescription
BoCaTFBS2006A 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.
PeakSeq2009A 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.


Allele-specific effects

Tool NameRelease DateDescription
AlleleSeq2011The 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.

Microarrays & Proteomics

Tool NameRelease DateDescription
ExpressYourself2003An interactive platform for background correction, normalization, scoring, and quality assessment of raw microarray data.
PARE2007(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.
ProCAT --BROKEN URL--2006A data analysis approach for protein microarrays. ProCAT corrects for background bias and spatial artifacts, identifies significant signals, filters nonspecific spots, and normalizes the resulting signal to protein abundance. ProCAT provides a powerful and flexible new approach for analyzing many types of protein microarrays.
Tilescope --BROKEN URL--2007An online analysis pipeline for high-density tiling microarray data. Tilescope normalizes signals between channels and across arrays, combines replicate experiments, score each array element, and identifies genomic features. The program is designed with a modular, three-tiered architecture, facilitating parallelism, and a graphic user-friendly interface, presenting results in an organized web page, downloadable for further analysis.
TilingNAA platform with all our tilling array analysis tools.


Clustering

Tool NameRelease DateDescription
Local Clustering2001A new algorithm for local clustering to find timeshifted and/or inverted relationships in gene expression data is available as C source code.

Network Tools

Tool NameRelease DateDescription
TopNet2004An automated web tool designed to calculate topological parameters and compare different sub-networks for any given network.
tYNA2006(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.
Yeasthub --BROKEN URL--???A semantic web-based application which demonstrates how a life sciences data warehouse can be built using a native Resource Description Framework (RDF) data store. This data warehouse allows integration of different types of yeast genome data provided by different resources in different formats including the tabular and RDF formats.


Evolution Tools

Tool NameRelease DateDescription
Coevolution analysis of protein residues2008An 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.


Genome Structural Variation Analysis

Tool NameRelease DateDescription
SVs2007-2011A dedicated web-page for analysis of genome structural variations (AGE, CNVnator, PEMer, BreakSeq, vcf2diploid).


Structural Biology Tools

Tool NameRelease DateDescription
Morph Server2000Generates a plausible pathway between two conformations of a protein or nucleic acid structure. A large number of statistics and several high-quality movies are output.
SPINE2001A laboratory-information management system (LIMS) for the NorthEast Structural Genomics Consortium. The online version is restricted to consortium users, but most of the code is freely available for download.
Macromolecular Packing Tools1994-2009A 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.
HIT2006(Helix Interaction Tool). A web-based comprehensive package of tools for analyzing helix-helix interactions in proteins.


Other

Tool NameRelease DateDescription
PubNet2005A 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. 
HUB???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.
Personal tools