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.
Software for DNA and amino acid editing, database management, plasmid maps, It can also be used for restriction and ligation, alignments, sequencer data import, calculators, gel image display, PCR, and more.
Proper citation: Gentle (RRID:SCR_016127) Copy
https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate
Software package for sequence alignment of pairwise sequence comparison. Exonerate can be used to align sequences using many alignment models, exhaustive dynamic programming, or a variety of heuristics., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Exonerate (RRID:SCR_016088) Copy
https://huttenhower.sph.harvard.edu/humann2
Software for profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data Used for millions of short DNA/RNA reads. This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members.
Proper citation: HUMAnN2 (RRID:SCR_016280) Copy
https://github.com/Teichlab/tracer
Software application for recovery of T cell receptor (TCR) data from single cell data. Used to reconstruct full-length, paired T cell receptor (TCR) sequences from T lymphocyte single-cell RNA sequence data. Links T cell specificity with functional response by revealing clonal relationships between cells alongside their transcriptional profiles.
Proper citation: TraCeR (RRID:SCR_016338) Copy
https://cm.jefferson.edu/rna22/
Software tool as a pattern based algorithm for detecting microRNA binding sites and their corresponding microRNA and mRNA complexes. Allows interactive exploration and visualization of miRNA target predictions. Permits link-out to external expression repositories and databases.
Proper citation: RNA22 (RRID:SCR_016507) Copy
https://www.genome.jp/tools/dinies/
Web server for predicting unknown drug-target interaction networks from various types of biological data in the framework of supervised network inference.
Proper citation: DINIES (RRID:SCR_016505) Copy
http://www.compbio.dundee.ac.uk/jpred/
Software tool for protein secondary structure prediction from the amino acid sequence by the JNet algorithm. Makes also predictions on Solvent Accessibility and Coiled-coil regions.
Proper citation: Jpred (RRID:SCR_016504) Copy
http://bioinf.bio.uth.gr/nat-ncs2
Web server for the detection and evolutionary classification of prokaryotic and eukaryotic nucleobase-cation symporters of the NAT/NCS2 family. Used to scan, identify and evolutionary classify NAT/NCS2 nucleobase transporter proteins.
Proper citation: NAT/NCS2 Hound (RRID:SCR_016473) Copy
https://genome.jgi.doe.gov/programs/fungi/1000fungalgenomes.jsf
Web application to provide genomic information for fungi. Includes sequenced fungal genomes, those in progress, and selected nominations. Nomination of new species for genome sequencing in the families or only one reference genome possible after providing DNA/RNA samples for their sequencing. Used to explore the diversity of fungi important for energy and the environment.
Proper citation: 1000 Fungal Genome Project (RRID:SCR_016463) Copy
https://github.com/WGS-TB/MentaLiST
Software for a MLST (multi-locus sequence typing) caller, based on a k-mer counting algorithm and written in the Julia language. Designed and implemented to handle large typing schemes.
Proper citation: MentaLiST (RRID:SCR_016469) Copy
http://www.ccb.jhu.edu/software/centrifuge/
Software for rapid and sensitive classification of metagenomic sequences. Used for the classification of DNA sequences from microbial samples and analysis of large metagenomics data sets on conventional desktop computers.
Proper citation: Centrifuge Classifier (RRID:SCR_016665) Copy
Collection of curated papillomavirus genomic sequences, accompanied by web-based sequence analysis tools. Database and web applications support the storage, annotation, analysis, and exchange of information.
Proper citation: PaVE (RRID:SCR_016599) Copy
https://www.ncbi.nlm.nih.gov/Web/Newsltr/Spring04/blastlab.html
Software tool as a program within the standalone BLAST package used to cluster either protein or nucleotide sequences. Used to make non redundant sequence sets.
Proper citation: BLASTClust (RRID:SCR_016641) Copy
https://www.ncbi.nlm.nih.gov/projects/genotyping/formpage.cgi
Web tool to identify the genotype of a viral sequence. A window is slid along the query sequence and each window is compared by BLAST to each of the reference sequences for a particular virus.
Proper citation: Genotyping (RRID:SCR_016645) Copy
https://www.ncbi.nlm.nih.gov/orffinder
Software tool to search for open reading frames (ORFs) in the DNA sequence. The program returns the range of each ORF, along with its protein translation. Used to search newly sequenced DNA for potential protein encoding segments, verify predicted protein. Limited to the subrange of the query sequence up to 50 kb long.
Proper citation: Open Reading Frame Finder (RRID:SCR_016643) Copy
https://github.com/iychoi/libra
Hadoop based tool for massive comparative metagenomics analysis. Compute the similarity between metagenomic samples.
Proper citation: Libra (RRID:SCR_016608) Copy
Web tool to import raw cDNA sequences, clean sequences, build sequence contigs, perform SignalP analysis, BLAST contigs against numerous BLAST databases, and view the results. Automates large scale cDNA sequence analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: dCAS (RRID:SCR_016612) Copy
https://github.com/santeripuranen/SuperDCA
Software tool for global direct coupling analysis of input genome alignments. Implements variant of pseudolikelihood maximization direct coupling analysis, with emphasis on optimizations that enable its use on genome scale. May be used to discover co evolving pairs of loci.Used for genome wide epistasis analysis.
Proper citation: SuperDCA (RRID:SCR_018175) Copy
Software for designing CRISPR/Cas guide RNA with reduced off target sites. Used for rational design of CRISPR/Cas target. Web server for selecting rational CRISPR/Cas targets from input sequence. Server currently incorporates genomic sequences of human, mouse, rat, marmoset, pig, chicken, frog, zebrafish, Ciona, fruit fly, silkworm, Caenorhabditis elegans, Arabidopsis, rice, Sorghum and budding yeast.
Proper citation: CRISPRdirect (RRID:SCR_018186) Copy
https://metacpan.org/pod/Bio::CUA
Software tool as flexible and comprehensive codon usage analyzer. Used to analyze codon usage bias (CUB) and relevant problems.
Proper citation: Codon Usage Analyzer (RRID:SCR_018500) 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 NIF Resources search. From here you can search through a compilation of resources used by NIF and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that NIF 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 NIF then you can log in from here to get additional features in NIF 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 NIF 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 NIF 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.
Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
