Tools   Select Another Resource Report Type

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://mirmap.ezlab.org/

Software application as an open source Pyton library to search and predict miRNA targets.

Proper citation: miRmap (RRID:SCR_016508) Copy   

•   Source: SciCrunch Registry

https://pave.niaid.nih.gov

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   

•   Source: SciCrunch Registry

https://github.com/vaklip/transfer_learning_ccnn

Software program to implement transfer learning for a connectome convolutional neural network trained to classify functional connectomes using Tensorflow.

Proper citation: transfer_ learning_ ccnn (RRID:SCR_016590) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://tbportals.niaid.nih.gov

Web based open access platform for global drug resistant tuberculosis data sharing and analysis. The NIAID TB Portals program and consortium of clinicians and scientists from countries with a heavy burden of TB, especially drug resistant TB, to collect TB data.

Proper citation: TB PORTALS (RRID:SCR_016594) Copy   

•   Source: SciCrunch Registry

https://pan.genomics.cn/ucdisk/s/VjuIRb&code=877833

Pipeline for construction and graphical visualization of annotated pangenome networks from microbial genomes. With the ability to extract and visualize gene contents and gene-gene physical adjacencies of a specific taxon from large-scale metagenomic data provides pangenome analysis to uncultured microbial taxa., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: MetaPGN (RRID:SCR_016472) Copy   

•   Source: SciCrunch Registry

https://nmrprocflow.org

Software as graphical and interactive tool dedicated to 1D spectra processing for NMR-based metabolomics.

Proper citation: NMRProcFlow (RRID:SCR_016592) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://gitlab.com/vtraver/PNNsMiceMachineVision

Data and code (Python) related to research paper: V. Javier Traver, Filiberto Pla, Marta Miquel, Maria Carbo-Gas, Isis Gil-Miravet, Julian Guarque-Chabrera "Cocaine-induced preference conditioning: a machine vision perspective".

Proper citation: PNNsMiceMachineVision (RRID:SCR_016485) Copy   

•   Source: SciCrunch Registry

http://ecogenomics.github.io/CheckM/

Software tool to assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes by using a broader set of marker genes specific to the position of a genome within a reference genome tree and information about the collocation of these genes.

Proper citation: CheckM (RRID:SCR_016646) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.flywings.org.uk/morphoj_page.htm

Software package written in Java for geometric morphometric analysis for two- and three-dimensional landmark data. Offers user-friendly environment for standard multivariate analyses such as principal components, discriminant analysis and multivariate regression as well as specialized applications including phylogenetics, quantitative genetics and analyses of modularity in shape data.

Proper citation: MorphoJ (RRID:SCR_016483) Copy   

•   Source: SciCrunch Registry

https://triage.niaid.nih.gov

Platform to facilitate prediction, analysis, and hypothesis generation from genome wide perturbation studies like those designed with RNAi and CRISPR technologies.

Proper citation: TRIAGE (RRID:SCR_016609) Copy   

•   Source: SciCrunch Registry

https://sleepdata.org/datasets/abc

Portal for randomized controlled trial to compare effectiveness of bariatric surgery versus continuous positive airway pressure (CPAP) therapy for obstructive sleep apnea. Signals included in the polysomnography (PSG) montage are EEG, EMG, EOG, ECG, SpO2, airflow, CPAP pressure, CPAP flow, plethysmography, position, pulse, light, respiratory effort, snore.

Proper citation: Apnea, Bariatric surgery, and CPAP study (RRID:SCR_016575) Copy   

•   Source: SciCrunch Registry

https://www.ncbi.nlm.nih.gov/projects/mutagene/

Software tool to explore and analyze mutagenic factors leading to tumors to decipher cancer genetic heterogeneity.

Proper citation: MutaGene (RRID:SCR_016574) Copy   

•   Source: SciCrunch Registry

https://bioinformatics.niaid.nih.gov/nglycpred/

Web based server to discriminate between glycosylated and non-glycosylated N-X-(T/S) sequons by incorporating structural information and patterns.

Proper citation: NGlycPred (RRID:SCR_016610) Copy   

•   Source: SciCrunch Registry

https://sleepdata.org/datasets/ccshs

Portal for population based pediatric cohorts studied with objective sleep studies. Includes children with in-home sleep studies, acoustic reflectometry, anthropometry, spirometry, blood pressure (BP), and neuropsychology (NP) and behavioral assessments. Signals recorded include EEG, ECG, EOG, EMG, SpO2, airflow (thermocouple) nasal pressure, respiratory effort, position, plethysmography, light, HR.

Proper citation: Cleveland Children's Sleep and Health Study (RRID:SCR_016584) Copy   

•   Source: SciCrunch Registry