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http://mummer.sourceforge.net/

Software package as system for rapidly aligning entire genomes. Alignment tool for DNA and protein sequences. Can align incomplete genomes.

Proper citation: MUMmer (RRID:SCR_018171) Copy   

•   Source: SciCrunch Registry

https://github.com/molgor/biospytial

Software package as spatial graph based computing engine for ecological big data. Modular open source knowledge engine designed to import, organize, analyse and visualize big spatial ecological datasets using power of graph theory. Handles species occurrences and their taxonomic classification for performing ecological analysis on biodiversity and species distributions. Data are linked with relationships that are stored in graph database, while tabular and geospatial data are stored in relational database management system.

Proper citation: biospytial (RRID:SCR_018226) Copy   

•   Source: SciCrunch Registry

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

Web server for quantitative prediction of peptide binding to any MHC molecule of known sequence using artificial neural networks. Characterizes binding specificity of given major histocompatibility complex molecule and predicts peptide length profile and peptide binding affinity. NetMHCpan 3.0 is improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length data sets. NetMHCpan 4.0 is trained on naturally eluted ligands and on peptide binding affinity data. NetMHCpan-4.1 server predicts binding of peptides to any MHC molecule of known sequence using artificial neural networks (ANNs).

Proper citation: NetMHCpan Server (RRID:SCR_018182) Copy   

•   Source: SciCrunch Registry

https://github.com/TomSexton00/4See

Software tool to visualize 4C data.

Proper citation: 4See (RRID:SCR_018014) Copy   

•   Source: SciCrunch Registry

https://github.com/sysu-yanglab/TDimpute

Software tool to transfer learning based deep neural network to impute missing gene expression data from DNA methylation data.

Proper citation: TDimpute (RRID:SCR_018306) Copy   

•   Source: SciCrunch Registry

https://github.com/shanemomara/omaraneurolab/tree/master/NeuroChaT

Software open source python toolbox to analyse neuronal signals recorded in vivo in freely behaving animal, with particular emphasis on spatial coding. Can be used as application programming interface, or as general user interface, and is designed to help simplify adoption of standardised analyses for behavioural neurophysiology and facilitate open data sharing and collaboration between laboratories.

Proper citation: NeuroChaT (RRID:SCR_018020) Copy   

•   Source: SciCrunch Registry

https://github.com/hangyabalazs/opeth

Software tool to enable flexible online visualization of action potential alignment to external events. Performs spike detection based on raw Open Ephys data exported via ZeroMQ. Requires triggers from Open Ephys for histogram display as spikes are detected around them.

Proper citation: Online Peri-Event Time Histogram for Open Ephys (RRID:SCR_018022) Copy   

•   Source: SciCrunch Registry

http://dgpred.cbr.su.se/

Web server to predict ΔGapp for membrane insertion of potential TM helix. Given amino acid sequence of putative transmembrane helix, server gives prediction of corresponding apparent free energy difference for insertion of this sequence into Endoplasmic Reticulum membrane by means of Sec61 translocon.

Proper citation: ΔG prediction server (RRID:SCR_018191) Copy   

•   Source: SciCrunch Registry

https://github.com/galaxyproteomics/mvpapplication-git.git

Software tool as plugin to enable viewing of results produced from workflows integrating genomic sequencing data and mass spectrometry proteomics data. Plugin to Galaxy bioinformatics workbench which enables visualization of mass spectrometry-based proteomics data integrated with genomic and/or transcriptomic sequencing data. Useful for verifying quality of results and characterizing novel peptide sequences identified using multi-omic proteogenomic approach.

Proper citation: Multi-omics Visualization Platform (RRID:SCR_018077) Copy   

•   Source: SciCrunch Registry

http://dichroweb.cryst.bbk.ac.uk/html/home.shtml

Web server for analysis of protein circular dichroism spectra. Provides access to circular dichroism secondary structure calculation algorithms and reference databases. Used in analysis of protein secondary structures.

Proper citation: DichroWeb (RRID:SCR_018125) Copy   

•   Source: SciCrunch Registry

https://web.expasy.org/protparam/

Software tool to calculate various physicochemical parameters for given protein stored in Swiss-Prot or TrEMBL or for user entered protein sequence. Protein can either be pecified as Swiss-Prot/TrEMBL accession number or ID, or in form of raw sequence. Computed parameters include molecular weight, theoretical pI, amino acid composition, atomic composition, extinction coefficient, estimated half-life, instability index, aliphatic index and grand average of hydropathicity.

Proper citation: ProtParam Tool (RRID:SCR_018087) Copy   

•   Source: SciCrunch Registry

https://www.machado.cnptia.embrapa.br/plantannot

Webserver for identifying targets for genetically modified crop breeding pipelines. Used to find proteins that have no annotation or function assigned and could be related to molecular mechanisms regarding abiotic stresses in plants. System aggregates orthology, coexpression networks and genomic data to filter genomes of plants downloaded from Phytozome and NCBI and select candidate proteins in that regard.

Proper citation: Plant Co-expression Annotation Resource (RRID:SCR_018429) 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://emboss.bioinformatics.nl/cgi-bin/emboss/pepwheel

Web tool to visualise protein sequences as helices. Draws helical wheel diagram for protein sequence. EMBOSS pepwheel displays peptide sequences in helical representation.

Proper citation: pepwheel (RRID:SCR_018398) 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

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

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://github.com/gevaertlab/BetaVAEImputation

Software tool as deep learning framework based on variational autoencoder to impute missing values in transcriptome and methylome data analysis.

Proper citation: betaVAEImputation (RRID:SCR_018730) Copy   

•   Source: SciCrunch Registry

http://pic.mbu.iisc.ernet.in

Web server for inter residue interaction calculations in single site. Determines accessible surface area and residue depth, which is distance of residue from surface of protein. Recognizes specific kind of interactions, such as apolar–apolar residue interactions or ionic interactions, that are formed between buried or exposed residues or near surface or deep inside. Recognizes interactions including disulphide bonds, hydrophobic interactions, ionic interactions, hydrogen bonds, aromatic- aromatic interactions, aromatic-sulphur interactions and cation interactions within protein or between proteins in complex.

Proper citation: Protein Interactions Calculator (RRID:SCR_018574) Copy   

•   Source: SciCrunch Registry