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| - | =Pseudogene Tools=
| + | Please refer to the [[Resources]] page. |
| - | [http://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 Biology Tools=
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| - | [http://molmovdb.org/molmovdb/morph Morph Server] generates 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. | + | |
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| - | [http://spine.nesg.org SPINE] is our 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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| - | A number of programs for calculating properties of protein and nucleic acid structures have been collected into a [http://geometry.molmovdb.org single distribution]. Included are a library of utility functions for dealing with structures, and a convenient interactive command-line interpreter.
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| - | [http://helix.gersteinlab.org/ HIT] (Helix Interaction Tool) is a web-based comprehensive package of tools for analyzing helix-helix interactions in proteins.
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| - | =Genome Technology Tools=
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| - | ===RNA-seq===
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| - | [http://act.gersteinlab.org/ ACT] (aggregation and correlation toolbox) is an aggregation and correlation toolbox for analyses of genome tracks.
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| - | [http://rnaseq.gersteinlab.org/fusionseq/ FusionSeq] is 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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| - | [http://code.google.com/p/iqseq/ IQSeq] is a tool for isoform quantification with RNA-seq data. Given isoform annotation and alignment of RNA-seq reads, it will use EM algorithm to infer the most probable expression level for each isoform of a gene.
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| - | [http://archive.gersteinlab.org/proj/rnaseq/rseqtools/ RSEQtools] is 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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| - | [http://www.gersteinlab.org/proj/BoCaTFBS/ BoCaTFBS] is 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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| - | [http://www.gersteinlab.org/proj/PeakSeq/ PeakSeq] is 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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| - | ===Microarrays & Proteomics===
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| - | [http://bioinfo.mbb.yale.edu/ExpressYourself ExpressYourself] is an interactive platform for background correction, normalization, scoring, and quality assessment of raw microarray data.
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| - | [http://proteomics.gersteinlab.org PARE] (Protein Abundance and mRNA Expression 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 are potentially worth further examination.
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| - | [http://purelight.biology.yale.edu:8080/servlets-examples/procat.html ProCAT] is a 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.
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| - | [http://tilescope.gersteinlab.org/ Tilescope] is an 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.
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| - | [http://tiling.gersteinlab.org Tiling] is a platform with all our tilling array analysis tools.
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| - | ===Clustering===
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| - | A new algorithm for [http://bioinfo.mbb.yale.edu/expression/cluster local clustering of expression data] to find timeshifted and/or inverted relationships is available as C source code.
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| - | =Network Tools=
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| - | [http://networks.gersteinlab.org/genome/interactions/networks/ TopNet] is an automated web tool designed to calculate topological parameters and compare different sub-networks for any given network.
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| - | [http://yeasthub.gersteinlab.org Yeasthub] is 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.
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| - | [http://tyna.gersteinlab.org/tyna/ tYNA] (TopNet-like Yale Network Analyzer) is 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 and Genomics Tools=
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| - | [http://coevolution.gersteinlab.org/coevolution/ Coevolution analysis of protein residues]: this is 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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| - | [http://act.gersteinlab.org/ ACT] (aggregation and correlation toolbox) is an aggregation and correlation toolbox for analyses of genome tracks.
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| - | [http://sv.gersteinlab.org SV] dedicated web-page for analysis of genome structural variations (AGE, CNVnator, PEMer, BreakSeq, vcf2diploid)
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| - | =Other=
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| - | [http://pubnet.gersteinlab.org/ PubNet] is 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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| - | [http://hub.gersteinlab.org/ir-supp/ HUB] is 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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