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/ArtRand/signalAlign
Software tool to align ionic current from MinION to reference sequence using trainable hidden Markov model. HMM-HDP models for MinION signal alignments,
Proper citation: signalalign (RRID:SCR_024339) Copy
http://www.bioinformatics.org/patristic/
Software Java program for calculating patristic distances and graphically comparing the components of genetic change.
Proper citation: Patristic (RRID:SCR_024154) Copy
https://docs.igdiscover.se/en/stable/
Software to analyze antibody repertoires and discover new V genes from high-throughput sequencing reads.Heavy chains, kappa and lambda light chains are supported (to discover VH, VK and VL genes)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: IgDiscover (RRID:SCR_024037) Copy
https://github.com/sanger-pathogens/iva
Software tool as de novo assembler designed to assemble virus genomes that have no repeat sequences,using Illumina read pairs sequenced from mixed populations at extremely high and variable depth.
Proper citation: IVA (RRID:SCR_024044) Copy
https://github.com/bioinfo-ut/PlasmidSeeker
Software tool as k-mer based program for identification of known plasmids from whole genome sequencing reads. Used for identification of known plasmids from bacterial whole genome sequencing reads.
Proper citation: PlasmidSeeker (RRID:SCR_024167) Copy
http://contra.stanford.edu/contrafold/
Software novel secondary structure prediction method based on conditional log-linear models, a flexible class of probabilistic models which generalize upon SCFGs by using discriminative training and feature-rich scoring. Used for sequence prediction.
Proper citation: CONTRAfold (RRID:SCR_023994) Copy
https://github.com/babinyurii/recan
Software tool as genetic distance plotting for recombination events analysis.
Proper citation: recan (RRID:SCR_024317) Copy
https://github.com/mourisl/Lighter
Software tool as kmer-based error correction method for whole genome sequencing data. Lighter uses sampling rather than counting to obtain set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors.
Proper citation: Lighter (RRID:SCR_024095) Copy
https://github.com/rrwick/Filtlong
Software tool for filtering long reads by quality.Can take set of long reads and produce smaller, better subset. Uses both read length and read identity when choosing which reads pass the filter.
Proper citation: Filtlong (RRID:SCR_024020) Copy
https://github.com/bioinfo-center-pasteur-fr/toppred
Software tool for membrane protein structure prediction.Transmembrane topology prediction.Used for predicting topology of bacterial inner membrane proteins.
Proper citation: toppred (RRID:SCR_024385) Copy
http://www.nematodes.org/bioinformatics/trace2dbEST/
Software tool to process raw sequenceing chromatograph trace files from EST projects into quality checked sequences, ready for submission to dbEST.
Proper citation: trace2dbEST (RRID:SCR_024386) Copy
https://github.com/sina-cb/Tn-seqExplorer
Software package written in Java for analysis of high-throughput sequencing data of transposon mutant libraries.Reads the alignment and the gene annotation, and provides the user with set of tools to investigate data and identify possibly essential or advantageous genes as those that contain significantly low counts of transposon insertions.
Proper citation: Tn-seq explorer (RRID:SCR_024387) Copy
http://saclab.tamu.edu/essentiality/transit/
Software tool for Himar1 TnSeq analysis.Provides graphical interface to three different statistical methods for analyzing TnSeq data. Used for identifying essential genes in individual datasets as well as comparative analysis between conditions.
Proper citation: TRANSIT (RRID:SCR_024389) Copy
Software tool to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood. Allows analysis of large data sets and automatically assigns estimations of support to each internal branch. Computes pairwise maximum likelihood distances as well as branch lengths for user specified trees.Conducts statistical tests on the data set.
Proper citation: TREE-PUZZLE (RRID:SCR_024382) Copy
https://rostlab.org/owiki/index.php/NORSp_-_predictor_of_NOn-Regular_Secondary_Structure
Online predictor of NOn-Regular Secondary Structure for disordered regions in protein. Used to predict long regions with no regular secondary structure. Upon user submission of protein sequence, NORSp will analyse the protein about its secondary structure, and presence of transmembrane helices and coiled-coil then return e-mail to user about the presence and position of disordered regions.
Proper citation: NORSp (RRID:SCR_024139) Copy
https://rostlab.org/owiki/index.php/Metastudent
Software tool to predict gene ontology terms for protein sequences through homology.
Proper citation: Metastudent (RRID:SCR_024110) Copy
https://github.com/Martinsos/edlib
Software C/C++ (and Python) library for sequence alignment using edit (Levenshtein) distance.
Proper citation: Edlib (RRID:SCR_024078) Copy
https://bitbucket.org/Glouvel/metabit/wiki/Home
Software pipeline for metagenomic and taxonomical analysis from shotgun sequencing.
Proper citation: metaBIT (RRID:SCR_024111) Copy
https://qtlreaper.sourceforge.net/
Software, written in C and compiled as Python module, for rapidly scanning microarray expression data for Quantitative Trait Locies. Searches for association between each expression trait and all genotypes and evaluates that association by permutation test. Performs bootstrap resampling to estimate confidence region for location of putative QTL.
Proper citation: qtlreaper (RRID:SCR_024199) Copy
https://mhap.readthedocs.io/en/stable/
Software tool as reference implementation of probabilistic sequence overlapping algorithm. Used to detect overlaps between noisy long-read sequence data.
Proper citation: MHAP (RRID:SCR_024113) 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 dkNET Resources search. From here you can search through a compilation of resources used by dkNET and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that dkNET 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 dkNET then you can log in from here to get additional features in dkNET 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 dkNET 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 dkNET 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.
The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
Email: info_at_ dknet.org
