From GersteinInfo

Below we highlight some of our tools and data sets. For an overview of tool-centric lab publications see our tools papers page. The source code of many of our tools in available on our lab Github page.

Contents 1 Tools portals 1.1 MolMovDB 1.2 Pseudogene.org 1.3 Networks 1.4 Structural Variants (SV) 2 Genome Technology Tools 2.1 Structural Variation 2.2 Functional Annotation 2.3 RNA-seq 2.4 ChiP 2.5 Allele-specific effects 2.6 Microarrays & Proteomics 3 Network Tools 4 Evolution Tools 5 Structure and Macromolecular Motions 6 Data sets 7 more tools

Tools portals

MolMovDB

Tool Name	Description
MolMovDB	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.

Pseudogene.org

Tool Name	Description
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.

Networks

Tool Name	Description
Networks	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.

Structural Variants (SV)

Tool Name	Description
Structural Variants	Structural Variations (SVs) and Copy Number Variations (CNVs) are a major source of genetic variation. our analysis tools are available in this portal.

Genome Technology Tools

Structural Variation

Tool Name	Release Date	Description
CNVnator (citation)	2013	An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing.
AGE	2013	AGE: defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision.

Functional Annotation

Tool Name	Release Date	Description
FunSeq	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.
VAT Github repo	2012	A computational framework to functionally annotate variants in personal genomes using a cloud-computing environment.

RNA-seq

Tool Name	Release Date	Description
FusionSeq Github repo	2011	FusionSeq: a modular framework for finding gene fusions by analyzing Paired-End RNA-Sequencing data.
ACT	2011	The aggregation and correlation toolbox (ACT) is an aggregation and correlation toolbox for analyses of genome tracks.
IQseq Github repo	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.
LESSeq Github repo	2013	Local Event-based analysis of alternative Splicing using RNA-Seq
RSEQtools	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.

ChiP

Tool Name	Release Date	Description
PeakSeq	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.

Allele-specific effects

Tool Name	Release Date	Description
AlleleSeq	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.

Microarrays & Proteomics

Tool Name	Release Date	Description
motips	2003	MOTIPS: Automated Motif Analysis for Predicting Targets of Modular Protein Domains.
PARE	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.

Network Tools

Tool Name	Release Date	Description
TopNet	2004	An automated web tool designed to calculate topological parameters and compare different sub-networks for any given network.
tYNA	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.
PubNet	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.

Evolution Tools

Tool Name	Release Date	Description
Coevolution analysis of protein residues	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.

Structure and Macromolecular Motions

Tool Name	Release Date	Description
Macromolecular Packing Tools	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.
3vee	1998	3vee is collection of program for the assessment of volumes in protein files.
geometry	1999	calculation of geometrical quantities associated with macromolecular structures and their motions
HIT	2006	(Helix Interaction Tool). A web-based comprehensive package of tools for analyzing helix-helix interactions in proteins.

Data sets

Tool Name	Release Date	Description
BreakDB	2008	This database, which is part of the PEMer package, contains information about structural variants and associated breakpoints.
DynaSIN	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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