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http://www.ebi.ac.uk/Tools/

The European Bioinformatics Institute (EBI) toolbox area provides a comprehensive range of tools for the field of bioinformatics. These are subdivided into categories in the left menu for convenience. EBI has developed a large number of very useful bioinformatics tools. A few examples include: - Similarity & Homology - the BLAST or FASTA programs can be used to look for sequence similarity and infer homology. - Protein Functional Analysis - InterProScan can be used to search for motifs in your protein sequence. - Proteomic Services NEW - UniProt DAS server allows researchers to show their research results in the context of UniProtKB/Swiss-Prot annotation. - Sequence Analysis - ClustalW2 a sequence alignment tool. - Structural Analysis - MSDfold can be used to query your protein structure and compare it to those in the Protein Data Bank (PDB). - Web Services - provide programmatic access to the various databases and retrieval/analysis services EBI provides. - Tools Miscellaneous - Expression Profiler a set of tools for clustering, analysis and visualization of gene expression and other genomic data. Sponsors: This resource is sponsored by EBI.

Proper citation: Toolbox at the European Bioinformatics Institute (RRID:SCR_002872) Copy   

•   Source: SciCrunch Registry

http://xgc.nci.nih.gov/

NIH initiative to support production of cDNA libraries, clones and 5'/3' sequences and to provide set of full-length (open reading frame) sequences and cDNA clones of expressed genes for Xenopus laevis and Xenopus tropicalis. Clones distribution is outsourced to for profit companies. Project concluded in September 2008. Resources generated by XGC are publicly accessible to biomedical research community. All sequences are deposited into GenBank.Corresponding clones are available through IMAGE clone distribution network. With conclusion of XGC project, GenBank records of XGC sequences will be frozen, without further updates. Since knowledge of what constitutes full-length coding region for some of genes and transcripts for which we have XGC clones will likely change in future, users planning to order XGC clones will need to monitor for these changes. Users can make use of genome browsers and gene-specific databases, such as UCSC Genome browser, NCBI's Map Viewer, and Entrez Gene, to view relevant regions of genome (browsers) or gene-related information (Entrez Gene).

Proper citation: Xenopus Gene Collection (RRID:SCR_007023) Copy   

•   Source: SciCrunch Registry

http://zgc.nci.nih.gov/

Part of zebrafish genome project. ZGC project to produce cDNA libraries, clones and sequences to provide complete set of full-length (open reading frame) sequences and cDNA clones of expressed genes for zebrafish. All ZGC sequences are deposited in GenBank and clones can be purchased from distributors of IMAGE consortium. With conclusion of ZGC project in September 2008, GenBank records of ZGC sequences will be frozen, without further updates. Since definition of what constitutes full-length coding region for some of genes and transcripts for which we have ZGC clones will likely change in future, users planning to order ZGC clones will need to monitor for these changes. Users can make use of genome browsers and gene-specific databases, such as UCSC Genome browser, NCBI's Map Viewer, and Entrez Gene, to view relevant regions of genome (browsers) or gene-related information (Entrez Gene).

Proper citation: Zebrafish Gene Collection (RRID:SCR_007054) Copy   

•   Source: SciCrunch Registry

https://web.uri.edu/riinbre/mic/

Core provides sequencing and bioinformatics support for INBRE and non-INBRE researchers. Provides data science services adjacent to traditional bioinformatics; access to computational and software resources for INBRE network institutions, particularly primarily undergraduate institutions; training for students and faculty in data science methods. Maintains professional network with other core and user facilities in Rhode Island and beyond to maximize resources available to our users.Utilizes novel technologies such as virtual/augmented reality for use in teaching and research.

Proper citation: Rhode Island INBRE Molecular Informatics Core Facility (RRID:SCR_017685) Copy   

•   Source: SciCrunch Registry

http://mgm.ku.edu/services

Research oriented service laboratory providing informatics support to research community. Services include data analysis and mining in proteomics, genomics and chemistry, systems biology approaches such as pathway, network and interaction analyses, large scale statistical and machine learning studies, protein structure, function and stability prediction, sequence and domain analyses,d esign and implementation of relational databases and software programs, consultation on experimental design involving data acquisition, management and analysis, report, grant, and manuscript preparation.

Proper citation: Kansas University at Lawrence Applied Bioinformatics Laboratory Core Facility (RRID:SCR_017751) Copy   

•   Source: SciCrunch Registry

http://genetics.group.shef.ac.uk/index.html

Core provides DNA sequencing services including DNA extraction, cell line identification, microsatellite analysis, and antibody sequencing,DNA Sequencing, Monoclonal Antibody Sequencing,Nucleic Acid Quantification,PCR Machine Hire,Real-Time PCR Robotic Liquid Handling,Taqman SNP Analysis.

Proper citation: University of Sheffield Genomic Core Facility (RRID:SCR_017912) Copy   

•   Source: SciCrunch Registry

http://athina.biol.uoa.gr/bioinformatics/waveTM/

A web tool for the prediction of transmembrane segments in alpha-helical membrane proteins. A sliding window of 20 residues is used in order to calculate an average residue hydrophobicity profile, using a hydrophobicity scale. Discrete Wavelet Transform is applied on the average residue hydrophobicity signal and the different frequency coefficients produced are adaptively thresholded so that a denoised signal is reconstructed. A dynamic programming algorithm processes the denoised signal to provide the optimal model for the number, the length and the location of membrane-spanning segments. The end points of the predicted segments are extended to include flanking hydrophobic residues. Topology prediction can also be obtained in conjunction with OrienTM (Liakopoulos et al, 2001). Analysis of a non-redundant test set, provides a ~95% per segment accuracy and ~90% per residue accuracy. Now, you can: * Run waveTM on a sequence * Browse the results obtained with the algorithm * View additional material concerning the hydrophobicity scale

Proper citation: waveTM (RRID:SCR_006199) Copy   

•   Source: SciCrunch Registry

http://igs-server.cnrs-mrs.fr/mgdb/Rickettsia/

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 18, 2016. Rickettsia are obligate intracellular bacteria living in arthropods. They occasionally cause diseases in humans. To understand their pathogenicity, physiologies and evolutionary mechanisms, RicBase is sequencing different species of Rickettsia. Up to now we have determined the genome sequences of R. conorii, R. felis, R. bellii, R. africae, and R. massiliae. The RicBase aims to organize the genomic data to assist followup studies of Rickettsia. This website contains information on R. conorii and R. prowazekii. A R. conorii and R. prowazekii comparative genome map is also available. Images of genome maps, dendrogram, and sequence alignment allow users to gain a visualization of the diagrams.

Proper citation: Rickettsia Genome Database (RRID:SCR_007102) Copy   

•   Source: SciCrunch Registry

http://athina.biol.uoa.gr/PRED-TMR/

A web server that predicts transmembrane domains in proteins using solely information contained in the sequence itself. The algorithm refines a standard hydrophobicity analysis with a detection of potential termini (edges, starts and ends) of transmembrane regions. This allows both to discard highly hydrophobic regions not delimited by clear start and end configurations and to confirm putative transmembrane segments not distinguishable by their hydrophobic composition. The accuracy obtained on a test set of 101 non homologous transmembranes proteins with reliable topologies compares well with that of other popular existing methods. Only a slight decrease in prediction accuracy was observed when the algorithm was applied to all transmembrane proteins of the SwissProt database (release 35).

Proper citation: PRED-TMR (RRID:SCR_006203) Copy   

•   Source: SciCrunch Registry

http://wwwmgs.bionet.nsc.ru/mgs/programs/panalyst/

WebProAnalyst provides web-accessible analysis for scanning the quantitative structure-activity relationships in protein families. It searches for a sequence region, whose substitutions are correlated with variations in the activities of a homologous protein set, the so-called activity modulating sites. WebProAnalyst allows users to search for the key physicochemical characteristics of the sites that affect the changes in protein activities. It enables the building of multiple linear regression and neural networks models that relate these characteristics to protein activities. WebProAnalyst implements multiple linear regression analysis, back propagation neural networks and the Structure-Activity Correlation/Determination Coefficient (SACC/SADC). A back propagation neural network is implemented as a two-layered network, one layer as input, the other as output (Rumelhart et al, 1986). WebProAnalyst uses alignment of amino acid sequences and data on protein activity (pK, Km, ED50, among others). The input data are the numerical values for the physicochemical characteristics of a site in the multiple alignment given by a slide window. The output data are the predicted activity values. The current version of WebProAnalyst handles a single activity for a single protein. The SACC/SADC may be defined as an estimate of the strongest multiple correlation between the physicochemical characteristics of a site in a multiple alignment and protein activities. The SACC/SADC coefficient makes possible the calculation of the possible highest correlation achievable for the quantitative relationship between the physicochemical properties of sites and protein activities. The SACC/SADC is a convenient means for an arrangement of positions by their functional significance. WebProAnalyst outputs a list of multiple alignment positions, the respective correlation values, also regression analysis parameters for the relationships between the amino acid physicochemical characteristics at these positions and the protein activity values.

Proper citation: Webproanalyst (RRID:SCR_008348) Copy   

•   Source: SciCrunch Registry

http://phylopythias.bifo.helmholtz-hzi.de/index.php?phase=wait

Web Server for Taxonomic Assignment of Metagenome Sequences that is a fast and accurate sequence composition-based classifier that utilizes the hierarchical relationships between clades. Taxonomic assignments with the web server can be made with a generic model, or with sample-specific models that users can specify and create. Several interactive visualization modes and multiple download formats allow quick and convenient analysis and downstream processing of taxonomic assignments.

Proper citation: PhyloPythiaS (RRID:SCR_011923) Copy   

•   Source: SciCrunch Registry

http://viewer.shigen.info/cgi-bin/crispr/crispr.cgi

Web tool to show micro homology sequences striding over double strand break point created by CRISPR/Cas9 system. Used to search for CRISPR target site with micro-homology sequences. Used to predict deletion pattern.

Proper citation: NBRP Medaka CRISPR target site (RRID:SCR_018159) Copy   

•   Source: SciCrunch Registry

http://cisbp.ccbr.utoronto.ca

Software tool as catalog of inferred sequence binding preferences. Online library of transcription factors and their DNA binding motifs.

Proper citation: CIS-BP (RRID:SCR_017236) Copy   

•   Source: SciCrunch Registry

http://nucleobytes.com/index.php/4peaks

Software application for viewing and editing sequence trace files.

Proper citation: 4Peaks (RRID:SCR_000015) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/science/tools/ssaha2-0

A program designed for the efficient mapping of sequence reads onto genomic references. The software is capable of reading most sequencing platforms and giving a range of outputs are supported.

Proper citation: Sequence Search and Alignment by Hashing Algorithm (RRID:SCR_000544) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.udel.edu/Research/skategenomeproject

Core facility provides a model for collaborative approaches to use specialized resources and expertise in an integrated process. Core builds on the expertise and resources provided by the Bioinformatics Cores of the five northeastern states that form NECC. The Skate Genome Annotation Workshops and Jamborees offer training and opportunities for faculty and students to work with and annotate genome sequences. Workshops include lectures, tutorials and exercises annotating the genome of the little skate, Leucoraja erinacea.

Proper citation: University of Delaware Skate Genome Project (RRID:SCR_005300) Copy   

•   Source: SciCrunch Registry

https://github.com/ekg/fastahack

Software application for indexing and extracting sequences and subsequences from FASTA files. It will only generate indexes for FASTA files in which the sequences have self-consistent line lengths.

Proper citation: Fastahack (RRID:SCR_016090) Copy   

•   Source: SciCrunch Registry

https://github.com/sanger-pathogens/Fastaq

Software application for diverse collection of scripts that perform useful and common FASTA/FASTQ manipulation tasks, such as filtering, merging, splitting, sorting, trimming, search/replace, etc. Input and output files can be gzipped (format is automatically detected) and individual Fastaq commands can be piped together.

Proper citation: Fastaq (RRID:SCR_016091) Copy   

•   Source: SciCrunch Registry

http://icebox.lbl.gov:8080/ApolloWebDemo/jbrowse/

WebApollo is an extensible web-based sequence annotation editor for community annotation. No software download is required and the annotations are saved to a centralized database with real-time annotation updating. (The edit server mediates annotation changes made by multiple users.) The Web based client uses JBrowse, is fast and highly interactive. WebApollo accesses many types of genomic data including access to public data from UCSC, Ensembl, and GMOD Chado databases. Source code (BSD License) * Client source code: https://github.com/berkeleybop/jbrowse * Annotation editing engine: http://code.google.com/p/apollo-web * Data model and I/O layer: http://code.google.com/p/gbol * Trellis server code: http://code.google.com/p/genomancer

Proper citation: WebApollo: A Web-Based Sequence Annotation Editor for Community Annotation (RRID:SCR_005321) Copy   

•   Source: SciCrunch Registry

http://www.ch.embnet.org/software/COILS_form.html

COILS is a program that compares a sequence to a database of known parallel two-stranded coiled-coils and derives a similarity score. By comparing this score to the distribution of scores in globular and coiled-coil proteins, the program then calculates the probability that the sequence will adopt a coiled-coil conformation.

Proper citation: COILS: Prediction of Coiled Coil Regions in Proteins (RRID:SCR_008440) Copy   

•   Source: SciCrunch Registry