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http://srv00.recas.ba.infn.it/atlas/index.html

Comprehensive database of A-to-I RNA Editing Events. Atlas of A-to-I RNA editing events in human and other organisms. Collection of A-to-I events in body sites of healthy individuals from GTEx project. RNA Editing sites can be searched by genomic region, gene name and other relevant features as tissue of origin. Query results are shown in sortable and downloadable tables in which main characteristics of individual RNA editing events are reported. RNA-Seq and DNA-Seq coverage per site as well as RNA editing levels are provided.

Proper citation: REDIportal (RRID:SCR_018490) Copy   

•   Source: SciCrunch Registry

https://github.com/zhanxw/MB-GAN

Software tool as deep learning simulation framework for simulating realistic microbiome data. Can automatically learn from given microbial abundances and compute simulated abundances that are indistinguishable from it.

Proper citation: MB-GAN (RRID:SCR_019289) 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

https://github.com/MikkelSchubert/adapterremoval

Software program to remove residual adapter sequences from next generation sequencing reads. Used for cleaning of next-generation sequencing reads. AdapterRemoval v2 introduces improvements in throughput, through use of single instruction, multiple data (SIMD; SSE1 and SSE2) instructions and multi-threading support; handles datasets containing reads or read-pairs with different adapters or adapter pairs; provides simultaneous demultiplexing and adapter trimming; has ability to reconstruct adapter sequences from paired-end reads for poorly documented data sets; provides native gzip and bzip2 support.

Proper citation: AdapterRemoval (RRID:SCR_011834) Copy   

•   Source: SciCrunch Registry

http://opm.phar.umich.edu/

Database that provides a collection of transmembrane, monotopic and peripheral proteins from the Protein Data Bank whose spatial arrangements in the lipid bilayer have been calculated theoretically and compared with experimental data. The database allows analysis, sorting and searching of membrane proteins based on their structural classification, species, destination membrane, numbers of transmembrane segments and subunits, numbers of secondary structures and the calculated hydrophobic thickness or tilt angle with respect to the bilayer normal.

Proper citation: Orientations of Proteins in Membranes database (RRID:SCR_011961) Copy   

•   Source: SciCrunch Registry

http://kmersvm.beerlab.org/

A webserver built on the Galaxy framework that enables the mining of sequence data for transcription factor binding sites. This tool suite was designed to aid in analysis of next-generation sequencing (NGS) data that uses a support vector machine (SVM) with kmer sequence features to identify predictive combinations of short transcription factor binding sites which determine the tissue specificity of the original NGS assay. While you may use datasets already available from Galaxy, you can upload your data using the ''Get Data'' Tool. The tool can upload data from a variety of locations.

Proper citation: kmer-SVM (RRID:SCR_010882) Copy   

•   Source: SciCrunch Registry

http://cpfp.sourceforge.net/

Software providing a data analysis pipeline for shotgun mass-spectrometry proteomics.

Proper citation: CPFP (RRID:SCR_012043) Copy   

•   Source: SciCrunch Registry

http://srna-workbench.cmp.uea.ac.uk/tools/visualisation-tools/vissr/

Software to generate a visual representation of sRNAs and user-imported genomic features. The tool may be run on its own or from other tools, e.g. miRCat.

Proper citation: VisSR (RRID:SCR_012024) Copy   

•   Source: SciCrunch Registry

http://www.geneprof.org/GeneProf/

A database of curated, integrated and reusable high-throughput genomics experiments and a web-based, graphical software suite that allows users to analyse data produced using high-throughput sequencing platforms (RNA-seq and ChIP-seq; Next-Generation Sequencing or NGS). Algorithm developers and computer programmers can develop their own modules and extend the functionality of GeneProf. Existing software can be easily wrapped and integrated in the GeneProf framework and data from GeneProf may be used externally.

Proper citation: GeneProf (RRID:SCR_012927) Copy   

•   Source: SciCrunch Registry

http://sift.bii.a-star.edu.sg/

Data analysis service to predict whether an amino acid substitution affects protein function based on sequence homology and the physical properties of amino acids. SIFT can be applied to naturally occurring nonsynonymous polymorphisms and laboratory-induced missense mutations. (entry from Genetic Analysis Software) Web service is also available.

Proper citation: SIFT (RRID:SCR_012813) Copy   

•   Source: SciCrunch Registry

http://www.guidetopharmacology.org

Portal and searchable database of pharmacological information. Information is presented at two levels, the initial view or landing pages for each target family provide expert-curated overviews of the key properties and the available selective ligands and tool compounds. For selected targets, more detailed introductory chapters for each family are available along with curated information on the pharmacological, physiological, structural, genetic and pathophysiogical properties of each target.

Proper citation: IUPHAR/BPS Guide to Pharmacology (RRID:SCR_013077) Copy   

•   Source: SciCrunch Registry

https://github.com/macs3-project/MACS

Software Python package for identifying transcript factor binding sites. Used to evaluate significance of enriched ChIP regions. Improves spatial resolution of binding sites through combining information of both sequencing tag position and orientation. Can be used for ChIP-Seq data alone, or with control sample with increase of specificity.

Proper citation: MACS (RRID:SCR_013291) Copy   

•   Source: SciCrunch Registry

http://genetics.bwh.harvard.edu/pph2/

Software tool which predicts possible impact of amino acid substitution on structure and function of human protein using straightforward physical and comparative considerations. PolyPhen-2 is new development of PolyPhen tool for annotating coding nonsynonymous SNPs.

Proper citation: PolyPhen: Polymorphism Phenotyping (RRID:SCR_013189) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.ai.sri.com/ptools/

A software application which supplies software tools to develop and maintain pathway/genome databases (PGDBs). These include the development of organism-specific databases, metabolic reconstruction and metabolic-flux modeling, scientific visualization and web publishing of organism-specific databases, analysis of gene-expression and metabolomics datasets, comparative genome and pathway analyses, and analysis of biological networks.

Proper citation: Pathway Tools (RRID:SCR_013786) Copy   

•   Source: SciCrunch Registry