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Displays large volumes of genomic rearrangement data. Circos is a visualization tool that applies a circular ideogram layout to display relationships between genomic intervals. The software provides a scalable means to illustrate relationships between genomic positions and is designed to allow flexible and easy rearrangement of elements in the image. It also contains several tools to help analyze, filter, and format data.
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Provides an analyser and browser tool for data expressed in multiple genomic coordinate systems. GenPlay can display RNA-seq, ChIP-seq, Methyl-seq, TimEX-seq and a variety of DNA sequence and annotation tracks. This software can used also for the evaluation of data aligned on custom genomes and offers a library of operations to process raw data. It enables data export into any of the coordinate systems that makeup the meta-reference genome.
A comparative genomic visualization tool that combines three complementary displays: (i) a table for thoroughly browsing amongst homologues, (ii) a comparator of orthologue functional annotations and (iii) a genomic organization view designed to improve the legibility of rearrangements and distinctive loci. The latter display combines symbolic and proportional graphical paradigms. Synchronized navigation across multiple species and interoperability between the views are core features of Insyght. A gene filter mechanism is provided that helps the user to build a biologically relevant gene set according to multiple criteria such as presence/absence of homologues and/or various annotations.
Provides a feature-rich set of comparative genomics tools for inspection of multiple genome structures, mining of orthologous gene families and identification of potential vaccine candidates. The Sybil suite of feature-rich web tools allows users to search and visualize several genomes based on clusters of orthologous genes. The views in Sybil are interactive allowing users to click on each drawn feature to retrieve more detailed information. Navigation between views is supported and provides Sybil with the unique ability to explore from the whole genome level to the protein and nucleotide multiple sequence alignment level without leaving the application. Export of tab-delimited tables, sequence data, and SVG and PDF publication-quality figures is possible from many of the views.
Supports an iterative process of multiplex mutation analysis and genome engineering. Millstone automates read alignment and variant calling using a hybrid reference-based and de novo assembly approach. It allows researchers to explore and compare mutations among genomic samples, and finally creates updated reference genomes and designs new genomic edits for subsequent rounds of experiments. The software allows researchers to investigate individual variants through interactive filtering and alignment visualization. It is deployable to a cloud platform, local cluster, or desktop.
Detects and visualizes structural variation from paired-end mapping data. Under this scheme, abnormally mapped read pairs are clustered based on the location of a gap signature. Several important features, including local depth of coverage, mapping quality and associated tandem repeat, are used to evaluate the quality of predicted structural variation. Compared with other approaches, it can detect many more large insertions and complex variants with lower false discovery rate. Moreover, inGAP-sv, written in Java programming language, provides a user-friendly interface and can be performed in multiple operating systems.
Generates reproducible maps of genes and genomes that can be used to generate publication-ready figures, starting from a wide range of formats. Since all the instructions for drawing the figures are contained in R code, genoPlotR is highly flexible, and thus it is straightforward to automate the process of drawing very similar figures for different datasets. The use of a scripting language makes it particularly suitable for integration into annotation and comparative genomics pipelines.
The Genetic Map Comparator
Compares genetic maps according to their key statistics and the relative positions of common markers. The Genetic Map Comparator allows users to compare maps via standard statistics (number of markers, average gap size between markers etc.) as well as to obtain a visual representation of the map congruences by plotting marker positions along chromosomes. The Genetic Map Comparator is able to import map files produced by most commonly used software for linkage analysis (e.g. Carthagene and JoinMap). The Genetic Map Comparator is a web-based application available online or for local use.
Creates an interactive overview visualization of the multiple genome alignment in a circular layout. GenomeRing is a highly interactive tool for multiple alignment visualization based on SuperGenome coordinates. The concept of the SuperGenome together with GenomeRing provides a quick and broad overview through the display of genomic events from completely aligned genomes and allows for a detailed analysis of specific genes through the linkage of GenomeRing to several other visualizations incorporated into Mayday, such as Mayday's genome browser.
MIG / Multi-Image Genome
A web-based application for visualizing, querying and filtering many thousands of genome browser regions as well as for exporting the data in a variety of formats. MIG allows the user to generate these collections in an automated way, and store multiple projects in the MIG database. These collections can also be shared with other MIG users so that whole groups can perform analysis on the same data. MIG has been used successfully to analyze ChIP-Seq data and RNA-Seq data and to detect somatic mutations in genome resequencing projects.
A web-based tool for viewing comparative genomic data. Gobe supports viewing multiple genomic regions simultaneously. Its simple text format and flash-based rendering make it an interactive, exploratory research tool. Gobe can be used without installation through our web service, or downloaded and customized with stylesheets and JavaScript callback functions. Gobe provides the basis for custom applications that utilize orthology and numerical data to reveal more about a region of interest.
Generates and visualizes clusters as a graph with accompanying statistics, evaluation metrics and associated background information. BlastGraph is a user-friendly application for comparative genomics analyses such as homologous sequence identification and clustering, phyletic patterns, genome phylogenetics, core gene identification and gene gain and loss. The user can check the coherence of a cluster, identify useful relationships (such as indels and fusion events) or gene types and interactively split and edit the cluster.
A Java-based bioinformatic application utilizing Standard Widget Toolkit/Swing graphics libraries and a SQLite database for performing visualized analyses of comparative genomics data in Brassicaceae (crucifer) plants. Compared with similar software and databases, one of the unique features of CrusView is its integration of karyotype information when comparing two genomes. This feature allows users to perform karyotype-based genome assembly and karyotype-assisted genome synteny analyses with preset karyotype patterns of the Brassicaceae genomes. Additionally, CrusView is a local program, which gives its users high flexibility when analyzing unpublished genomes and allows users to upload self-defined genomic information so that they can visually study the associations between genome structural variations and genetic elements, including chromosomal rearrangements, genomic macrosynteny, gene families, high-frequency recombination sites, and tandem and segmental duplications between related species.
Aquerium / Architecture Querying Podium
Visualizes genomic presence and absence of biomolecules with a focus on protein domain architectures. Aquerium offers advanced domain organization querying against the database of pre-computed domains for ~26,000 organisms and it can be utilized for identification of evolutionary events, such as fusion, disassociation, duplication, and shuffling of protein domains. The tool also allows alternative inputs of custom entries or BLASTP results for visualization. Aquerium will be a useful tool for biologists who perform comparative genomic and evolutionary analyses.
Compares multiple genomes and performs sensitivity analysis for synteny block detection and for the subsequent computation of reversal distances. Cinteny can also be used to interactively browse syntenic blocks conserved in multiple genomes, to facilitate genome annotation and validation of assemblies for newly sequenced genomes, and to construct and assess phylogenomic trees. In particular, Cinteny provides: i) integration of synteny browsing with assessment of evolutionary distances for multiple genomes; ii) flexibility to adjust the parameters and re-compute the results on-the-fly; iii) ability to work with user provided data, such as orthologous genes, sequence tags or other conserved markers.
Organizes genomic contexts into branching diagrams. To facilitate genomic context analysis, it implements Graphical User Interface (GUI) features, such as text search filtering, point-and-click interrogation of individual contexts, and genomic visualization via a multi-genome browser. JContextExplorer has been designed to develop a general-purpose genomic context comparison platform to both (i) generate context trees and (ii) facilitate genomic exploration through our multi-genome browser interface.
VISTA Browser
A Java applet, very efficient for interactively visualizing results of comparative sequence analysis in the VISTA format on the scale of whole chromosomes along with annotations. The user may select any genome as the reference or base, and display the level of conservation between this reference and the sequences of another species in a particular interval. A user can use default values for conservation cutoffs (X% over Y bp), or specify them. Conserved regions are highlighted under the curve, with different colors used for coding and noncoding sequences. The browser has a number of options, such as zoom, extraction of a region to be displayed, user-defined parameters for conservation level, and options for selecting sequence elements to study. VISTA Browser is realized as a dynamic web-interface synchronized with the central MySQL.
3D Genome Tuner
Enables comparing circular genomes in a 3D space. 3D Genome Tuner is a hybrid of circular map and comparative map tools. Its capability of viewing comparisons between multiple circular maps in a 3D space offers great benefits to the study of comparative genomics. It is an interactive application and provides real-time visualization. 3D Genome Tuner provides one navigation window and five sub-windows that allow user to explore detailed genomic features. The navigation window is a tree control that expands on every genome as well as every feature.
PatSeq Finder
Allows users to conduct sequence searches. PatSeq Finder allows users to identify, compare and analyze patents disclosing genetic sequences similar to a sequence of interest. It includes multiple functionalities such as: (i) an integrated view of both patent and sequence information; (ii) filtering and conservation of results and documents into collections; (iii) marking and labelling of results; (iv) browsing family information; and (v) downloading related information including original patent documents. It is part of the PatSeq toolkit.
GECKO-MGV / Multi Genome Viewer
A web app to display, browse and analyse the results of genome comparison produced by GECKO and GECKO-CSB. This tool is composed of several independent modules that execute specific tasks for the application: files, canvas and matrices. GECKO-MGV integrates functionality for zooming, filtering and selecting fragments. A novel interesting feature of this tool is the integration of the evolutionary events timeline. GECKO-MGV is a part of GECKO software suite.
Facilitates human judgement about gene annotations by visualizing blast hits in contigs and chromosomes. Plot-hits is an application that checks annotations of de novo assembly of algal eukaryotic parasite Amoeboaphelidium protococcarum genome. The two sets of output data are displayed in coordinates of a contig/chromosome: (i) one that contains gene coordinates from a contig or a chromosome annotation and (ii) the other contains blast hits of the contig or the chromosome search against protein database.
BOV / BLAST Output Visualization
Allows users to interactively visualize the matching regions of query and database hit sequences, thereby allowing the user to quickly and easily dissect complex matching patterns. BOV extracts the alignment coordinates of matching regions between the query and the corresponding database hit sequence. It provides a user-friendly web interface to visualize the standard BLAST output for investigating wide-ranging genomic problems, including single query and batch query datasets. The tool is valuable to users interested in identifying regions of co-linearity, duplication, translocation, and inversion among sequences.
CAGO / Comparative Analysis of Genome Organization
Provides an interactive genome atlas. CAGO provides a platform gathering dynamic exploratory and signal analysis features in a genome atlas tool to analyze genomic properties. The application contains an automatic pipeline, a file-based data repository, a SVG converter, and three web interfaces. It can be used for determining the application of autocorrelation and cross-correlation to detect rhythmic patterns of a genomic property as well as assist users in generating and testing various hypothesis.
A visualization suite that consists of the Circular Genome Viewer, Stack Map, ChromoMap, Dot Plot, and Viral Viewer. MEDEA is a suite of Adobe Flash based comparative genomic : the MEDEA Circular Genome Viewer brings together genomic feature densities and genome alignments in an overview that reflects the physical structure of circular genomes; the MEDEA Stack Map provides a linear view of genome features of one or more sequences; the MEDEA ChromoMap visualizes pre-computed genome alignments (regions of genomic similarity) between a single reference genome and one or more other genomes; the MEDEA Dot Plot displays the synteny between a reference sequence and a number of user- selected query sequences.
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