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https://github.com/nch-igm/rna-stability

Software tool as parallel processing framework for large scale generation of secondary RNA structures and folding statistics for transcriptome of any species.

Proper citation: rna-stability (RRID:SCR_019259) Copy   

•   Source: SciCrunch Registry

https://github.com/brentp/mosdepth

Software command line tool for rapidly calculating genome wide sequencing coverage. Measures depth from BAM or CRAM files at either each nucleotide position in genome or for sets of genomic regions. Used for fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing quick coverage calculation for genomes and exomes.

Proper citation: mosdepth (RRID:SCR_018929) Copy   

•   Source: SciCrunch Registry

https://radar-base.org/index.php/home/about-us/

Open source mobile health platform for collecting, monitoring, and analyzing data using sensors, wearables, and mobile devices. Enables study design and set up, active and passive remote data collection, secure data transmission via Wifi and/or Bluetooth and scalable solutions for data storage, management and access. Allows study participants to share their health data with clinicians and researchers in secure way.

Proper citation: RADAR-base (RRID:SCR_019233) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://elastix.isi.uu.nl/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 23,2023. Software toolbox for rigid and nonrigid registration of images. elastix is open source software, based on the well-known 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. A paper describing elastix contains more details: S. Klein, M. Staring, K. Murphy, M.A. Viergever, J.P.W. Pluim, elastix: a toolbox for intensity based medical image registration,; IEEE Transactions on Medical Imaging, vol. 29, no. 1, pp. 196 - 205, January 2010., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: elastix (RRID:SCR_009619) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/IMGT-ONTOLOGY

Ontology for immunogenetics and immunoinformatics. Provides semantic specification of terms to be used in immunogenetics and immunoinformatics and manages related knowledge, thus allowing standardization for immunogenetics data from genome, proteome, genetics, two-dimensional (2D) and three-dimensional (3D) structures. Manages the knowledge through diverse facets relying on seven axioms, IDENTIFICATION, CLASSIFICATION, DESCRIPTION, NUMEROTATION, LOCALIZATION, ORIENTATION and OBTENTION. These axioms postulate that any object, any process and any relation can be identified, classified, described, numbered, localized and orientated, and the way it is obtained can be characterized. The axioms constitute the Formal IMGT-ONTOLOGY, also designated as IMGT-Kaleidoscope. As the same axioms can be used to generate concepts for multi-scale level approaches, the Formal IMGT-ONTOLOGY represents a paradigm for system biology ontologies, which need to identify, to classify, to describe, to number, to localize and to orientate objects, processes and relations at the molecule, cell, tissue, organ, organism or population levels. IMGT, the international ImMunoGeneTics information system, has been built on IMGT-ONTOLOGY. The version 1.0.2 of IMGT-ONTOLOGY includes the concepts of IDENTIFICATION and the concepts of CLASSIFICATION.

Proper citation: IMGT-ONTOLOGY (RRID:SCR_010342) Copy   

•   Source: SciCrunch Registry

http://evexdb.org

EVEX is a text mining resource built on top of PubMed abstracts and PubMed Central full texts. It contains over 40 million bio-molecular events among more than 76 million automatically extracted gene/protein name mentions. The text mining data further has been enriched with gene normalization results, allowing straightforward integration with external resources. Further, gene families from Ensembl and HomoloGene provide homology-based event generalizations. EVEX presents both direct and indirect associations between genes and proteins, enabling explorative browsing of relevant literature.

Proper citation: Evex (RRID:SCR_010509) Copy   

•   Source: SciCrunch Registry

http://mirdb.org/miRDB/

An online database for miRNA target prediction and functional annotations.

Proper citation: miRDB (RRID:SCR_010848) Copy   

•   Source: SciCrunch Registry

http://ccb.jhu.edu/software/glimmer/index.shtml

A software system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses.

Proper citation: Glimmer (RRID:SCR_011931) Copy   

•   Source: SciCrunch Registry

http://mafft.cbrc.jp/alignment/server/

Software package as multiple alignment program for amino acid or nucleotide sequences. Can align up to 500 sequences or maximum file size of 1 MB. First version of MAFFT used algorithm based on progressive alignment, in which sequences were clustered with help of Fast Fourier Transform. Subsequent versions have added other algorithms and modes of operation, including options for faster alignment of large numbers of sequences, higher accuracy alignments, alignment of non-coding RNA sequences, and addition of new sequences to existing alignments.

Proper citation: MAFFT (RRID:SCR_011811) Copy   

•   Source: SciCrunch Registry

http://www.uhnresearch.ca/labs/tillier/ProDesign/ProDesign.html

Webserver that can be used to find oligonucleotide probe sets for microarray slides. The probes can be for individual sequences or for clusters of genes. This webserver accepts files up to 200 kb in size in order to minimize the running time. For larger files please download the program.

Proper citation: ProDesign (RRID:SCR_010966) Copy   

•   Source: SciCrunch Registry

http://www.g-language.org/GenomeProjector/

A searchable database browser with zoomable user interface using Google Map API. Genome Projector currently contains 4 views: Genome map, Plasmid map, Pathway map, and DNA walk.

Proper citation: Genome Projector (RRID:SCR_011790) Copy   

•   Source: SciCrunch Registry

http://www.jcvi.org/metarep/

A tool for high-performance comparative metagenomics that allows users to view, query, browse, and compare metagenomics annotation profiles from short reads or assemblies. Users can use statistical tests, hierarchical clustering, multidimensional scaling, and heat maps to compare multiple datasets at various functional and taxonomic levels.

Proper citation: METAREP (RRID:SCR_011926) Copy   

•   Source: SciCrunch Registry

http://plntfdb.bio.uni-potsdam.de

Public database arising from efforts to identify and catalogue all plant genes involved in transcriptional control.Integrative plant transcription factor database that provides web interface to access large sets of transcription factors of several plant species, currently encompassing Arabidopsis thaliana (thale cress), Populus trichocarpa (poplar), Oryza sativa (rice), Chlamydomonas reinhardtii and Ostreococcus tauri. Provides access point to its daughter databases of species-centered representation of transcription factors (OstreoTFDB, ChlamyTFDB, ArabTFDB, PoplarTFDB and RiceTFDB). Information including protein sequences, coding regions, genomic sequences, expressed sequence tags, domain architecture and scientific literature is provided for each family.

Proper citation: PlnTFDB (RRID:SCR_010899) Copy   

•   Source: SciCrunch Registry

http://darwin.uvigo.es/software/prottest_server.html

Web-based software used for the selection of best-fit models of protein evolution., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: ProtTest (RRID:SCR_014628) Copy   

•   Source: SciCrunch Registry

http://fatcat.burnham.org/

Web server for flexible protein structure comparison. Structure alignment is formulated as the aligned fragment pairs chaining process allowing at most t twists, and the flexible structure alignment is transformed into a rigid structure alignment when t is forced to be 0., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: FATCAT (RRID:SCR_014631) Copy   

•   Source: SciCrunch Registry

http://compbio.mit.edu/cummeRbund/index.html

Software R package used for simplifying and analyzing Cufflink RNA-Seq output. This program takes various output files from a cuffdiff run and creates a SQLite database of the results that will describe the appropriate relationships between the genes, transcripts, transcription start sites and CDS regions.

Proper citation: CummeRbund (RRID:SCR_014568) Copy   

•   Source: SciCrunch Registry