Tools   Select Another Resource Report Type

http://www.prognoscan.org/

Database for meta analysis of prognostic value of genes from server at Kyushu Institute of Technology. Collection of publicly available cancer microarray datasets with clinical annotation, as well as tool for assessing biological relationship between gene expression and prognosis. Provides platform for evaluating potential tumor markers and therapeutic targets.

Proper citation: PrognoScan (RRID:SCR_018740) Copy   

•   Source: SciCrunch Registry

https://evcouplings.org/

Web server provides functional and structural information about proteins from their evolutionary record using methods from statistical physics. Computes evolutionary couplings from sequence alignments and predicts 3D structure for your protein of interest. Allows to run former EVcouplings, EVmutation, EVfold and EVcomplex jobs.

Proper citation: Evolutionary Couplings Server (RRID:SCR_018745) Copy   

•   Source: SciCrunch Registry

http://crispr-era.stanford.edu/index.jsp

Software comprehensive design tool for CRISPR mediated gene editing, repression and activation. Fast and comprehensive guide RNA design tool for genome editing, repression and activation. Used for automated genome wide sgRNA design.

Proper citation: CRISPR-ERA (RRID:SCR_018710) Copy   

•   Source: SciCrunch Registry

http://galaxy.seoklab.org/

Web server for protein structure prediction and refinement. Used to predict protein structure from sequence by template based modeling. Used for refinement after providing starting model structure and locations of loops or termini to be refined.

Proper citation: GalaxyWEB (RRID:SCR_018558) Copy   

•   Source: SciCrunch Registry

http://www.cbs.dtu.dk/services/MaxAlign/

Web tool for maximizing usable data in alignment. Maximizes number of characters that are present in gap free columns alignment area by selecting optimal subset of sequences. Removes sequences with many gaps in post process of alignments in order to improve alignment area.

Proper citation: MaxAlign (RRID:SCR_018552) Copy   

•   Source: SciCrunch Registry

https://milaboratory.com/software/mixcr/

Software tool to processes big immunome data from raw sequences to quantitated clonotypes by MiLaboratory LLC. Universal software for analysis of T- and B-cell receptor repertoire high throughput sequencing data. Software for comprehensive adaptive immunity profiling.

Proper citation: MiXCR (RRID:SCR_018725) Copy   

•   Source: SciCrunch Registry

http://huanglab.phys.hust.edu.cn/hpepdock/

Web server for blind peptide protein docking based on hierarchical algorithm. Blind peptide-protein docking by fast modeling of peptide conformations and global sampling of binding orientations.

Proper citation: HPEPDOCK Server (RRID:SCR_018561) Copy   

•   Source: SciCrunch Registry

https://www.bcforms.org

Software toolkit for concretely describing non-canonical polymers and complexes to facilitate global biochemical networks. Web tool for describing molecular structure of macromolecular complexes, including non canonical monomeric forms, circular topologies, and crosslinks. Describes semantic meaning of whole cell computational models.

Proper citation: BcForms (RRID:SCR_018654) Copy   

•   Source: SciCrunch Registry

http://galaxy.seoklab.org/cgi-bin/submit.cgi?type=REFINE

Web server for protein structure prediction, refinement, and related methods. First rebuilds side chains and performs side-chain repacking and subsequent overall structure relaxation by molecular dynamics simulation.

Proper citation: GalaxyRefine (RRID:SCR_018531) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/EpiEstim/index.html

Framework and software to estimate time varying reproduction numbers during epidemics. Tools to quantify transmissibility throughout epidemic from analysis of time series of incidence. Used to estimate time varying instantaneous reproduction numbers from incidence time series.

Proper citation: EpiEstim (RRID:SCR_018538) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/package=precrec

Software R package for fast and accurate precision recall and ROC curve calculations. Calculates accurate precision recall and Receiver Operator Characteristics curves.

Proper citation: precrec (RRID:SCR_018659) Copy   

•   Source: SciCrunch Registry

https://www.datanator.info

Software toolkit for discovering data needed to build, calibrate, and validate mechanistic models of cells. Integrated database of molecular data for quantitatively modeling cellular behavior. Web application for identifying relevant data for modeling specific organism in specific environmental condition.

Proper citation: Datanator (RRID:SCR_018651) Copy   

•   Source: SciCrunch Registry

https://www.ncbi.nlm.nih.gov/Structure/bwrpsb/bwrpsb.cgi

Web tool for detection of structural and functional domains in protein sequences. Allows computation and download of conserved domain annotation for large sets of protein queries. Allows to view results graphically. Shows domain footprints, alignment details, and conserved features on any individual query sequence.

Proper citation: Batch Web CD-Search Tool (RRID:SCR_018756) Copy   

•   Source: SciCrunch Registry

http://www.vmatch.de/

Software tool for efficiently solving large scale sequence matching tasks.

Proper citation: Vmatch (RRID:SCR_018968) Copy   

•   Source: SciCrunch Registry

https://github.com/oushujun/LTR_FINDER_parallel

Software tool for parallelization of LTR_FINDER enabling rapid identification of long terminal repeat retrotransposons.

Proper citation: LTR_FINDER_parallel (RRID:SCR_018969) Copy   

•   Source: SciCrunch Registry

https://github.com/SouthGreenPlatform/metaXplor

Web interfaced application to store, share, explore and manipulate metagenomic data. Interactive viral and microbial metagenomic data manager. Stores large volumes of user defined sample, sequence and assignment information while providing filtering web interface. Offers means to share datasets with collaborators, BLAST external sequences against them, and confirm assignments by running phylogenetic placement. Available as set of Docker containers that make it simple to deploy on various infrastructures.

Proper citation: metaXplor (RRID:SCR_019025) Copy   

•   Source: SciCrunch Registry

https://github.com/LCSB-BioCore/GigaSOM.jl

Software tool for huge scale, high performance flow cytometry data clustering and visualization in Julia. High performance clustering and visualization of huge cytometry datasets.

Proper citation: GigaSOM.jl (RRID:SCR_019020) Copy   

•   Source: SciCrunch Registry

https://github.com/acg-team/tral

Software tool to make annotation of tandem repeats in amino acid and nucleic data simple. Includes modules for detecting tandem repeats with both de novo software and sequence profile HMMs. Used for statistical significance analysis of putative tandem repeats, and filtering of redundant predictions.

Proper citation: TRAL (RRID:SCR_018979) Copy   

•   Source: SciCrunch Registry

http://crdd.osdd.net/raghava/vicmpred/index.html

Software tool as SVM based method for prediction of functional proteins of gram negative bacteria using amino acid patterns and composition. Webserver for functional classification of proteins of bacteria into virulence factors, information molecule, cellular process and metabolism molecule.

Proper citation: VICMpred (RRID:SCR_019039) Copy   

•   Source: SciCrunch Registry

http://annotree.uwaterloo.ca/

Web tool for visualization of genome annotations across large phylogenetic trees.Used for visualization and exploration of functionally annotated microbial tree of life. Integrates taxonomic, phylogenetic and functional annotation data from bacterial and archaeal genomes.

Proper citation: Annotree (RRID:SCR_018980) Copy   

•   Source: SciCrunch Registry