Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
https://github.com/mahmoudibrahim/JAMM
Software tool as peak finder for joint analysis of NGS replicates. Used for peak finding in next generation sequencing broad and narrow datasets like ChIP-Seq, ATAC-Seq, DNase-Seq. Can integrate information from biological replicates and assign peak boundaries accurately.
Proper citation: JAMM (RRID:SCR_017049) Copy
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
http://www.cbs.dtu.dk/services/NetPhos/
Web tool as artificial neural network method that predicts phosphorylation sites in independent sequences. Web application based on determination of activity of protein kinases using in vitro assays with either naturally occurring peptides or synthetic peptides. NetPhos 3.1 server predicts serine, threonine or tyrosine phosphorylation sites in eukaryotic proteins using ensembles of neural networks. Both generic and kinase specific predictions are performed. Generic predictions are identical to predictions performed by NetPhos 2.0. Kinase specific predictions are identical to predictions by NetPhosK 1.0. NetPhos 3.1 is available as stand-alone software package.
Proper citation: NetPhos (RRID:SCR_017975) Copy
http://bioinformatics.uni-muenster.de/tools/nanopipe2
Web tool for analysis of MinION (ONT) long sequencing reads. Used for analysis of reads generated by the Oxford Nanopore sequencing devices. Provides alignments to any target of interest, alignment statistics and information about polymorphisms.
Proper citation: NanoPipe (RRID:SCR_016852) Copy
http://deweylab.biostat.wisc.edu/detonate/
Software tool to evaluate de novo transcriptome assemblies from RNA-Seq data. Consists of RSEM-EVAL and REF-EVAL packages. RSEM-EVAL is reference-free evaluation method. REF-EVAL is reference based and can be used to compare sets of any kinds of genomic sequences.
Proper citation: DETONATE (RRID:SCR_017035) Copy
Database that describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds. This specialist database is dedicated to the display and analysis of genomic, structural and biochemical information on Carbohydrate-Active Enzymes (CAZymes). CAZy data are accessible either by browsing sequence-based families or by browsing the content of genomes in carbohydrate-active enzymes. New genomes are added regularly shortly after they appear in the daily releases of GenBank. New families are created based on published evidence for the activity of at least one member of the family and all families are regularly updated, both in content and in description. An original aspect of the CAZy database is its attempt to cover all carbohydrate-active enzymes across organisms and across subfields of glycosciences. One can search for CAZY Family pages using the Protein Accession (Genpept Accession, Uniprot Accession or PDB ID), Cazy family name or EC number. In addition, genomes can be searched using the NCBI TaxID. This search can be complemented by Google-based searches on the CAZy site.
Proper citation: CAZy- Carbohydrate Active Enzyme (RRID:SCR_012909) Copy
http://www.cbs.dtu.dk/services/ProP/
Web application which predicts arginine and lysine propeptide cleavage sites in eukaryotic protein sequences using an ensemble of neural networks. Furin-specific prediction is the default. It is also possible to perform a general proprotein convertase prediction.
Proper citation: ProP Server (RRID:SCR_014936) Copy
Web tool for discovery and visualization of differences in amino acid composition. Two samples of amino acid sequences serve as input and a bar chart composed of twenty data points is output.
Proper citation: Composition Profiler (RRID:SCR_014630) Copy
http://www.ebi.ac.uk/Tools/psa/genewise/
Gene alignment tool from the EBI which predicts gene structure using similar protein sequences. See also the associated GenomeWise tool.
Proper citation: GeneWise (RRID:SCR_015054) Copy
https://bitbucket.org/genomicepidemiology/kma/src/master/
Software mapping method designed to map raw reads directly against redundant databases, in an ultra-fast manner using seed and extend.Used for aligning high quality reads against highly redundant databases, where unique matches often does not exist. Works for long low quality reads as well, such as those from Nanopore. Non-unique matches are resolved using the "ConClave" sorting scheme, and a consensus sequence are outputtet in addition to other common attributes, based on users demands.
Proper citation: KMA (RRID:SCR_024054) Copy
https://posit.co/products/open-source/shinyserver/
Open Source platform to host multiple Shiny applications on single server.
Proper citation: shiny-server (RRID:SCR_024334) Copy
Software parallel local alignment search tool for database comparison. NGS sequence similarity search tool providing significant accelerations of seeds based heuristic comparison methods.
Proper citation: PLAST (RRID:SCR_024170) Copy
https://github.com/ahmedmoustafa/JAligner
Open source software Java implementation of the Needleman�Wunsch and Smith-Waterman algorithms for biological pairwise sequence alignment with the affine gap penalty model.
Proper citation: JAligner (RRID:SCR_024050) Copy
https://seqan.github.io/lambda/
Software tool as local aligner optimized for many query sequences and searches in protein space. It is compatible to BLAST, but much faster than BLAST and many other comparable tools.
Proper citation: Lambda (RRID:SCR_024052) Copy
https://github.com/cboursnell/crb-blast
Software tool for finding orthologs between one set of sequences and another. This is particularly useful in genome and transcriptome annotation.
Proper citation: crb-blast (RRID:SCR_024325) Copy
Software for alignment free sequence comparison. Uses pattern of care and don't care positions. Compares frequencies of spaced words according to pre-defined pattern.
Proper citation: spaced (RRID:SCR_024345) Copy
Pattern matching grammar language and set of tools to search pattern in sequence nucleic or proteic.
Proper citation: Logol (RRID:SCR_024104) Copy
https://gitlab.com/rki_bioinformatics/purple
Software tool for selecting target specific peptide candidates directly from given proteome sequence data.
Proper citation: purple (RRID:SCR_024183) Copy
http://bioinf.spbau.ru/sibelia
Software comparative genomics tool to assist biologists in analysing genomic variations that correlate with pathogens, or genomic changes that help microorganisms adapt in different environments. Used for evolutionary and genome rearrangement studies for multiple strains of microorganisms.
Proper citation: sibelia (RRID:SCR_024336) Copy
https://sibsim4.sourceforge.net/
Software tool designed to align expressed DNA sequence with genomic sequence, allowing for introns.
Proper citation: sibsim4 (RRID:SCR_024338) Copy
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the RRID Resources search. From here you can search through a compilation of resources used by RRID and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that RRID has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on RRID then you can log in from here to get additional features in RRID such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
You can save any searches you perform for quick access to later from here.
We recognized your search term and included synonyms and inferred terms along side your term to help get the data you are looking for.
If you are logged into RRID you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the sources that were queried against in your search that you can investigate further.
Here are the categories present within RRID that you can filter your data on
Here are the subcategories present within this category that you can filter your data on
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
