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Web tool for discovery and visualization of differences in amino acid composition. Two samples of amino acid sequences serve as input and a bar chart composed of twenty data points is output.
Proper citation: Composition Profiler (RRID:SCR_014630) Copy
Database that describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds. This specialist database is dedicated to the display and analysis of genomic, structural and biochemical information on Carbohydrate-Active Enzymes (CAZymes). CAZy data are accessible either by browsing sequence-based families or by browsing the content of genomes in carbohydrate-active enzymes. New genomes are added regularly shortly after they appear in the daily releases of GenBank. New families are created based on published evidence for the activity of at least one member of the family and all families are regularly updated, both in content and in description. An original aspect of the CAZy database is its attempt to cover all carbohydrate-active enzymes across organisms and across subfields of glycosciences. One can search for CAZY Family pages using the Protein Accession (Genpept Accession, Uniprot Accession or PDB ID), Cazy family name or EC number. In addition, genomes can be searched using the NCBI TaxID. This search can be complemented by Google-based searches on the CAZy site.
Proper citation: CAZy- Carbohydrate Active Enzyme (RRID:SCR_012909) Copy
http://www.cbs.dtu.dk/services/ProP/
Web application which predicts arginine and lysine propeptide cleavage sites in eukaryotic protein sequences using an ensemble of neural networks. Furin-specific prediction is the default. It is also possible to perform a general proprotein convertase prediction.
Proper citation: ProP Server (RRID:SCR_014936) Copy
http://www.ebi.ac.uk/Tools/psa/genewise/
Gene alignment tool from the EBI which predicts gene structure using similar protein sequences. See also the associated GenomeWise tool.
Proper citation: GeneWise (RRID:SCR_015054) Copy
Web tool for display, annotation and management of phylogenetic trees. Accessible with any modern web browser.
Proper citation: iTOL (RRID:SCR_018174) Copy
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
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
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
https://laniakea-elixir-it.github.io/
Software tool for automatic deployment of virtual Galaxy environments for life science. Can be deployed over common cloud architectures supported both by public and private e-infrastructures. User interacts with Laniakea based service through simple front end that allows general setup of Galaxy instance, then Laniakea takes care of automatic deployment of virtual hardware and software components. User gains access with full administrative privileges to private, production grade, fully customized, Galaxy virtual instance, and to underlying virtual machine.
Proper citation: Laniakea (RRID:SCR_018146) Copy
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
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
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
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
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
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
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
Web tool to perform gene set enrichment testing. Used to test for predefined biologically relevant gene sets that contain more significant genes from experimental dataset than expected by chance. Logistic regression approach for identifying enriched biological groups in gene expression data.
Proper citation: LRPath (RRID:SCR_018572) Copy
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
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
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
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