BOL: Related items

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/

Harvest: a suite of core-genome alignment and visualization tools

Jit — Fri, 08 Dec 2017 07:16:03 -0600

Harvest is a suite of core-genome alignment and visualization tools for quickly analyzing thousands of intraspecific microbial genomes, including variant calls, recombination detection, and phylogenetic trees.

Tools

Parsnp - Core-genome alignment and analysis
Gingr - Interactive visualization of alignments, trees and variants
HarvestTools - Archiving and postprocessing

Address of the bookmark: https://harvest.readthedocs.io/en/latest/

AliTV—interactive visualization of whole genome comparisons

Jit — Wed, 10 Jan 2018 07:08:17 -0600

AliTV, which provides interactive visualization of whole genome alignments. AliTV reads multiple whole genome alignments or automatically generates alignments from the provided data. Optional feature annotations and phylo- genetic information are supported. The user-friendly, web-browser based and highly customizable interface allows rapid exploration and manipulation of the visualized data as well as the export of publication-ready high-quality figures. AliTV is freely available at https://github.com/AliTVTeam/AliTV

https://alitvteam.github.io/AliTV/

Address of the bookmark: https://github.com/AliTVTeam/AliTV

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/

Mulan: Multiple-sequence local alignment and visualization for studying function and evolution

Jit — Fri, 24 Aug 2018 09:50:01 -0500

Mulan: Multiple-sequence local alignment and visualization for studying function and evolution

Mulan (http://mulan.dcode.org/), a novel method and a network server for comparing multiple draft and finished-quality sequences to identify functional elements conserved over evolutionary time. Mulan brings together several novel algorithms: the TBA multi-aligner program for rapid identification of local sequence conservation, and the multiTF program for detecting evolutionarily conserved transcription factor binding sites in multiple alignments. In addition, Mulan supports two-way communication with the GALA database; alignments of multiple species dynamically generated in GALA can be viewed in Mulan, and conserved transcription factor binding sites identified with Mulan/multiTF can be integrated and overlaid with extensive genome annotation data using GALA.

Address of the bookmark: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC540288/

GfaViz: flexible and interactive visualization of GFA sequence graphs

Jit — Thu, 23 Jan 2020 07:33:46 -0600

GFA (Graphical Fragment Assembly) is an emerging standard format for representing sequence graphs. Although it was originally conceived as a format for sequence assembly (hence the name), and this remains its core application, it is more general, and able to represent many different types of sequence graphs, including scaffolding graphs, alignment graphs, variant graphs and splicing graphs.

Address of the bookmark: https://github.com/ggonnella/gfaviz

Circos visualization !

BioStar — Mon, 06 Mar 2023 06:01:32 -0600

Circos visualization

https://wlcb.oit.uci.edu/modules/index.html

Address of the bookmark: https://wlcb.oit.uci.edu/NG-Circos

A web-based tool for sequence alignment statistics and innovative visualization

BioStar — Thu, 04 Apr 2024 01:44:50 -0500

AlignStatPlot, a new R package and online tool that is well-documented and easy-to usefor MSA and post-MSA analysis. This tool performs both traditional and cutting-edge analy-ses on sequencing data and generates new visualisation methods for MSA results. Whencompared to currently available tools, AlignStatPlot provides a robust ability to handle andvisualise diversity data, while the online version will save time and encourage researchersto focus on explaining their findings. It is a simple tool that can be used in conjunction withpopulation genetics software (PDF) AlignStatPlot: An R package and online tool for robust sequence alignment statistics and innovative visualization of big data.

Address of the bookmark: https://bioinformatics.um6p.ma/AlignStatPlot/