BOL: Related items

GMOL: An Interactive Tool for 3D Genome Structure Visualization

Jit — Wed, 21 Mar 2018 12:25:20 -0500

GMOL was developed based upon our multi-scale approach that allows a user to scale between six separate levels within the genome. With GMOL, a user can choose any unit at any scale and scale it up or down to visualize its structure and retrieve corresponding genome sequences.

Address of the bookmark: https://www.nature.com/articles/srep20802

D-GENIES: A tool for Dotplot large Genomes in an Interactive, Efficient and Simple way

Jit — Mon, 11 Jun 2018 09:41:22 -0500

D-GENIES – for Dotplot large Genomes in an Interactive, Efficient and Simple way – is an online tool designed to compare two genomes. It supports large genome and you can interact with the dot plot to improve the visualisation. We use minimap version 2 to align the two genomes. Then, the PAF file is parsed and plotted into an interactive plot written with d3.js library. D-Genies also allows to display dot plots from other aligners by uploading their PAF or MAF alignment file. http://dgenies.toulouse.inra.fr/

Address of the bookmark: http://dgenies.toulouse.inra.fr/

UpSetR: An R Package for the Visualization of Intersecting Sets and their Properties

BioStar — Mon, 28 Jan 2019 18:38:44 -0600

UpSetR generates static UpSet plots. The UpSet technique visualizes set intersections in a matrix layout and introduces aggregates based on groupings and queries. The matrix layout enables the effective representation of associated data, such as the number of elements in the aggregates and intersections, as well as additional summary statistics derived from subset or element attributes.

For further details about the original technique see the UpSet website. You can also check out the UpSetR shiny app. Here is the source code for the shiny wrapper.

A Python package called py-upset to create UpSet plots has been created by GitHub user ImSoErgodic.

Address of the bookmark: https://github.com/hms-dbmi/UpSetR/

SynVisio: An Interactive Multiscale Synteny Visualization Tool for McScanX.

Jit — Sun, 31 May 2020 02:01:14 -0500

SynVisio lets you explore the results of McScanX a popular synteny and collinearity detection toolkit and generate publication ready images.

SynVisio requires two files to run:

The simplified gff file that was used as an input for a McScanX query.
The collinearity file generated as an output by McScanX for the same input query.
Optional track file in bedgraph format to annotate the generated charts.

SynVisio offers different types of visualizations such as Linear Parallel plots, Hive plots, Stacked Parallel Plots and Dot plots. Users can configure the type of plots required and then choose the source and the target chromosomes that need to be mapped. Users also have option to download the generated visualizations in publication ready SVG or PNG formats.

Address of the bookmark: https://synvisio.github.io/#/

Comprehensive list of visualization tools for biological pathways

Neel — Tue, 30 Jan 2018 06:01:31 -0600

The study of biological pathways is a key to understand the different processes inside a cell: proteins exert their function not in isolation but in a tightly controlled network of interactions and reactions. Activation of a pathway typically leads to a change of state in the cell. Pathways come in different flavors, depending on their functions in the cell – the three main types are metabolic pathways, gene regulatory pathways, and signaling pathways. These biological pathways and networks are not only an appropriate approach to visualize molecular reactions. They have also become one leading method in -omics data analysis and visualization.

Following are the comprehensive list of visualization tools for biological pathways:

BiNA

Drawings of metabolic networks supporting hiding of cofactors and drawing of chemical structures

http://bina.unipax.info/

BioTapestry

Interactive tool for building, visualizing and sharing gene regulatory network models over the web

http://www.biotapestry.org/

Caleydo

Visual analysis framework targeted at biomolecular data. Visualization of interdependencies between multiple datasets

http://www.caleydo.org/

CellDesigner

A modeling tool for biochemical networks

http://www.celldesigner.org/

Edinburgh Pathway Editor

Edit and draw pathway diagrams

http://epe.sourceforge.net/SourceForge/EPE.html

GenMAPP

Visualization of gene expression and other genomic data on maps representing biological pathways and groupings of genes

http://www.genmapp.org/

Ingenuity IPA

Data integration platform and manually annotated pathways

http://tinyurl.com/IngenuityPath

JDesigner

Graphical modeling environment for biochemical reaction networks

http://jdesigner.sourceforge.net/Site/JDesigner.html

KaPPA View

Plant pathways

http://kpv.kazusa.or.jp/

KEGG Atlas

Interactive Kyoto Encyclopedia of Genes and Genomes pathways

http://www.genome.jp/kegg/

Omix

Visualizing multi-omics data in metabolic networks

https://www.omix-visualization.com

PathVisio

Biological pathway analysis software that allows drawing, editing and analysis of biological pathways

http://www.pathvisio.org/

VitaPad

Application to visualize biological pathways and map experimental data to them

http://tinyurl.com/vitapad/

Web tools for pathways

ArrayXPath

Mapping and visualizing microarray gene-expression data and integrated biological pathway resources using SVG

http://tinyurl.com/ArrayXPath/

GEPAT

Integrated analysis of transcriptome data in genomic, proteomic and metabolic contexts

http://gepat.sourceforge.net/

iPath

Web-based tool for the visualization, analysis and customization of pathway maps

http://pathways.embl.de/

Kegg-Based Viewer

KEGG-based pathway visualization tool for complex high-throughput data

http://www.g-language.org/data/marray/

MapMan

User-driven tool that displays large datasets onto diagrams of metabolic pathways or other processes

http://mapman.gabipd.org/web/guest/mapman

MetPA

Analysis and visualization of metabolomic data within the biological context of metabolic pathways

http://metpa.metabolomics.ca

Omics Viewer

Data mapping on BioCyc pathways (collection of 5500 pathway/genome databases)

http://www.biocyc.org/

Pathway Explorer

Interactive Java drawing tool for the construction of biological pathway diagrams in a visual way and the annotation of the components and interactions between them

http://genome.tugraz.at/pathwayexplorer/pathwayexplorer_description.shtml

Pathway projector

Zoomable pathway browser using KEGG atlas and Google Maps API

http://www.g-language.org/PathwayProjector/

PATIKA

Integrated environment composed of a central database and a visual editor, built around an extensive ontology and an integration framework

http://www.cs.bilkent.edu.tr/~patikaweb/

Reactome SkyPainter

Visualization of over-represented pathways and reactions from gene lists

http://www.reactome.org/skypainter-2

WikiPathways

Wiki-based, open, public platform dedicated to the curation of biological pathways by and for the scientific community

http://www.wikipathways.org/

Bandage: interactive visualization of de novo genome assemblies

Shruti Paniwala — Mon, 04 Dec 2017 10:09:37 -0600

Bandage (a Bioinformatics Application for Navigating De novo Assembly Graphs Easily) is a tool for visualizing assembly graphs with connections. Users can zoom in to specific areas of the graph and interact with it by moving nodes, adding labels, changing colors and extracting sequences. BLAST searches can be performed within the Bandage graphical user interface and the hits are displayed as highlights in the graph. By displaying connections between contigs, Bandage presents new possibilities for analyzing de novo assemblies that are not possible through investigation of contigs alone.

Availability and implementation: Source code and binaries are freely available at https://github.com/rrwick/Bandage. Bandage is implemented in C++ and supported on Linux, OS X and Windows. A full feature list and screenshots are available at http://rrwick.github.io/Bandage.

Address of the bookmark: http://rrwick.github.io/Bandage/

xmatchview: smith-waterman alignment visualization

Rahul Nayak — Thu, 28 Dec 2017 09:00:58 -0600

xmatchview and xmatchview-conifer are imaging tools for comparing the synteny between DNA sequences. It allows users to align 2 DNA sequences in fasta format using cross_match and displays the alignment in a variety of image formats. xmatchview and xmatchview-conifer are written in python and run on linux and windows. They serve as visual tools for analyzing cross_match alignments. Cross_match (Green, P. (1994) http://www.phrap.org) uses an implementation of the Smith-Waterman algorithm for comparing DNA sequences that is sensitive.

http://www.bcgsc.ca/platform/bioinfo/software/xmatchview

Address of the bookmark: https://github.com/warrenlr/xmatchview

assemblytics: delta file to analyze alignments of an assembly to another assembly or a reference genome

Jit — Thu, 14 Jun 2018 07:31:00 -0500

Download and install MUMmer Align your assembly to a reference genome using nucmer (from MUMmer package) $ nucmer -maxmatch -l 100 -c 500 REFERENCE.fa ASSEMBLY.fa -prefix OUT Consult the MUMmer manual if you encounter problems Optional: Gzip the delta file to speed up upload (usually 2-4X faster) $ gzip OUT.delta Then use the OUT.delta.gz file for upload. Upload the .delta or delta.gz file (view example) to Assemblytics Important: Use only contigs rather than scaffolds from the assembly. This will prevent false positives when the number of Ns in the scaffolded sequence does not match perfectly to the distance in the reference. The unique sequence length required represents an anchor for determining if a sequence is unique enough to safely call variants from, which is an alternative to the mapping quality filter for read alignment. http://assemblytics.com/

Address of the bookmark: http://assemblytics.com/

NanoPack: visualizing and processing long-read sequencing data

Jit — Fri, 10 Aug 2018 18:41:34 -0500

The NanoPack tools are written in Python3 and released under the GNU GPL3.0 License. The source code can be found at https://github.com/wdecoster/nanopack, together with links to separate scripts and their documentation. The scripts are compatible with Linux, Mac OS and the MS Windows 10 subsystem for Linux and are available as a graphical user interface, a web service at http://nanoplot.bioinf.be and command line tools.

https://academic.oup.com/bioinformatics/article/34/15/2666/4934939

Address of the bookmark: https://github.com/wdecoster/nanoQC

Environment for Tree Exploration (ETE) is a Python programming toolkit that assists in the recontruction, manipulation, analysis and visualization of phylogenetic trees

Rahul Nayak — Wed, 27 Nov 2019 05:32:33 -0600

The Environment for Tree Exploration (ETE) is a Python programming toolkit that assists in the recontruction, manipulation, analysis and visualization of phylogenetic trees (although clustering trees or any other tree-like data structure are also supported).

Other tools

https://github.com/shenwei356/taxonkit

ETE, version: 3.1.1
BioPython, version: 1.73
taxadb, version: 0.10.1
TaxonKit, version: 0.5.0

Address of the bookmark: https://pypi.org/project/ete3/3.1.1/