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https://bioconductor.org/packages/genomation/

Software R package for simplfiying common tasks in genomic feature analysis. Toolkit to summarize, annotate and visualize genomic intervals. Provides functions for reading BED and GFF files as GRanges objects, summarizing genomic features over predefined windows so users can make average enrichment of features over defined regions or produce heatmaps. Can annotate given regions with other genomic features such as exons,introns and promoters.

Proper citation: genomation (RRID:SCR_003435) Copy   

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http://gepat.sourceforge.net/

A web-based software tool offering an integrated analysis of transcriptome data under genomic, proteomic and metabolic context.

Proper citation: GEPAT (RRID:SCR_003597) Copy   

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http://jexpress.bioinfo.no/site/

Gene expression analysis software using Java.

Proper citation: J-Express (RRID:SCR_003609) Copy   

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http://ophid.utoronto.ca/navigator/

A software package for visualizing and analyzing protein-protein interaction networks. NAViGaTOR can query OPHID / I2D - online databases of interaction data - and display networks in 2D or 3D. To improve scalability and performance, NAViGaTOR combines Java with OpenGL to provide a 2D/3D visualization system on multiple hardware platforms. NAViGaTOR also provides analytical capabilities and supports standard import and export formats such as GO and the Proteomics Standards Initiative (PSI). NAViGaTOR can be installed and run on Microsoft Windows, Linux / UNIX, and Mac OS systems. NAViGaTOR is written in Java and uses JOGL (Java bindings for OpenGL) to support scalability, highlighting or suppressing of information, and other advanced graphic approaches.

Proper citation: Network Analysis, Visualization and Graphing TORonto (RRID:SCR_008373) Copy   

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http://emboss.sourceforge.net/

Software analysis package for molecular biology community. Automatically copes with data in variety of formats and allows transparent retrieval of sequence data from web. Libraries are provided with package. Provides toolkit for creating bioinformatics applications or workflows. Provides set of sequence analysis programs. Provided programs cover areas such as sequence alignment, rapid database searching with sequence patterns, protein motif identification, nucleotide sequence pattern analysis, codon usage analysis for small genomes, rapid identification of sequence patterns in large scale sequence sets, and presentation tools for publication.

Proper citation: EMBOSS (RRID:SCR_008493) Copy   

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http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi

This server provides programs, web services, and databases, related to our work on RNA secondary structures. For general information and other offerings from our group see the main TBI web server. With the 1st of May 2009 we updated our servers to the Vienna RNA package version 1.8.2! The Vienna RNA Servers: * RNAfold server predicts minimum free energy structures and base pair probabilities from single RNA or DNA sequences. * RNAalifold server predicts consensus secondary structures from an alignment of several related RNA or DNA sequences. You need to upload an alignment. * RNAinverse server allows you to design RNA sequences for any desired target secondary structure. * RNAcofold server allows you to predict the secondary structure of a dimer. * RNAup server allows you to predict the accessibility of a target region. * LocARNA server generates structural alignments from a set of sequences. In collaboration with the Bioinformatics Group Freiburg. * barriers server allows you to get insights into RNA folding kinetics. * RNAz server will assist you in detecting thermodynamically stable and evolutionarily conserved RNA secondary structures in multiple sequence alignments. * Structure conservation analysis server will assist you in detecting evolutionarily conserved RNA secondary structures in multiple sequence alignments. * RNAstrand server allows you to predict the reading direction of evolutionarily conserved RNA secondary structures. * RNAxs server assists you in siRNA design. * Bcheck predicts rnpB genes Downloads Get the Source code for: * the Vienna RNA Package, our basic RNA secondary structure analysis software. * The ALIDOT package for finding conserved structure motifs (add-on) * The barriers program for analysis of RNA folding landscapes. Databases * Atlas of conserved Viral RNA Structures found by ALIDOT

Proper citation: Vienna RNA (RRID:SCR_008550) Copy   

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http://lowelab.ucsc.edu/tRNAscan-SE

Web server to search for tRNA genes in genomic sequence. If you would like to run tRNAscan-SE locally, you can get the UNIX source code (gzip''d tar file).

Proper citation: tRNAscan-SE (RRID:SCR_008637) Copy   

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http://steps.sourceforge.net/STEPS/default.php

STEPS is a package for exact stochastic simulation of reaction-diffusion systems in realistic, complex 3D geometries. Our core simulation algorithm is an efficient implementation of a variation on Gillespie''s SSA, extended to deal with diffusion of molecules over the elements of a 3D tetrahedral mesh. While it was mainly developed for simulating detailed models of neuronal signaling pathways in dendrites and around synapses, it is a general tool and can be used for studying any biochemical pathway in which spatial gradients and morphology are thought to play a role. We have implemented STEPS as a set of Python modules, which means STEPS users can use Python scripts to control all aspects of setting up the model, generating a mesh, controlling the simulation and generating and analyzing output. The core computational routines are still implemented as C/C++ extension modules for maximal speed of execution.

Proper citation: STEPS (RRID:SCR_008742) Copy   

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http://iubio.bio.indiana.edu:8089/

Provides summary of gene and genomic information from eukaryotic organism databases. This includes gene symbol and full name, chromosome, genetic and molecular map information, Gene Ontology (Function/Location/Process) and gene homology, product information, links to extended gene information.

Proper citation: Eukaryote Genes (RRID:SCR_008617) Copy   

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http://cbil.upenn.edu/RUM/

An alignment, junction calling, and feature quantification pipeline specifically designed for Illumina RNA-Seq data.

Proper citation: RUM (RRID:SCR_008818) Copy   

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https://github.com/armintoepfer/QuasiRecomb/releases

A jumping hidden Markov model that describes the generation of the viral quasispecies and a method to infer its parameters by analysing next generation sequencing data.

Proper citation: QuasiRecomb (RRID:SCR_008812) Copy   

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https://genome.unc.edu/xpn/

Merging Two Gene Expression Studies via Cross Platform Normalization.

Proper citation: XPN (RRID:SCR_008845) Copy   

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http://tvap.genome.wustl.edu/tools/music/

A set of tools aimed at determining the significance of somatic mutations discovered within a given cohort of cancer samples, incorporating the cohort''s alignment data, variant lists and any relevant clinical data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: MuSiC (RRID:SCR_008792) Copy   

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http://research-pub.gene.com/gmap/

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. A software program for mapping and aligning cDNA sequences to a genome. The program maps and aligns a single sequence with minimal startup time and memory requirements, and provides fast batch processing of large sequence sets. The program generates accurate gene structures, even in the presence of substantial polymorphisms and sequence errors, without using probabilistic splice site models. Methodology underlying the program includes a minimal sampling strategy for genomic mapping, oligomer chaining for approximate alignment, sandwich DP for splice site detection, and microexon identification with statistical significance testing.

Proper citation: GMAP (RRID:SCR_008992) Copy   

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http://bioinfo.au.tsinghua.edu.cn/software/seqsaw/

A package for mapping of spliced reads and unbiased detection of novel splice junctions from RNA-seq data.

Proper citation: SeqSaw (RRID:SCR_009185) Copy   

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http://wpicr.wpic.pitt.edu/WPICCompGen/bars.htm

Software application that is a statistical method that bridges the gap between single-locus and haplotype-based tests of association. It is based on the non-parametric regression techniques embodied by Bayesian Adaptive Regression Splines. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: BARS (RRID:SCR_009123) Copy   

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http://www.cbs.dtu.dk/services/NetOGlyc/

Server that produces predictions of mucin-type GalNAc O-glycosylation sites in mammalian proteins.

Proper citation: NetOGlyc (RRID:SCR_009026) Copy   

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https://github.com/SuperElastix/elastix

Software toolbox for rigid and nonrigid registration of images. Software, based on Insight Segmentation and Registration Toolkit (ITK). The software consists of a collection of algorithms that are commonly used to solve (medical) image registration problems. The modular design of elastix allows the user to quickly configure, test, and compare different registration methods for a specific application. A command-line interface enables automated processing of large numbers of data sets, by means of scripting.

Proper citation: elastix (RRID:SCR_009619) Copy   

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http://mocklerlab.org/tools/1

An application for discovering potential splice junctions in high throughput sequencing (HTS) data.

Proper citation: Supersplat (RRID:SCR_009826) Copy   

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http://bioinf.cs.ucl.ac.uk/psipred/

Web tool as secondary structure prediction method, incorporating two feed forward neural networks which perform analysis on output obtained from PSI-BLAST. Web server offering analyses of protein sequences.

Proper citation: PSIPRED (RRID:SCR_010246) Copy   

•   Source: SciCrunch Registry