MoDMaps3D - Main Menu

Welcome to MoDMaps3D!

MoDMaps3D is a general-purpose interactive tool that can compute and display the interrelationships within any set of biological, simulated, or synthetic DNA sequences, closely related or completely unrelated, of the same length or of different lengths, several kbp-long or complete genomes. Here are some of the things you can do with three dimensional Molecular Distance Maps.

Explore a Map: Explore available built-in MoDMaps. These maps provide extensive information for each genomic sequence involved in each map, along with complementary information.
Build or Extend a Map: Build a new MoDMap from scratch tailored to your dataset. Include up to 12 categories, with as many sequences you need in each of them. Alternatively, extend a MoDMap adding your points. You can select a "base" map from a variety of available maps and then add your DNA sequences in it.
Compute a distance: Compute the distance between any two DNA sequences, given as NCBI accession numbers.

Explore available MoDMaps

Here you can find a list of available built-in MoDMaps to explore. Select a map from sidebar, preview its content, and click on "Show Map" to see it in action.

Build your map, for your dataset

Choose an option to continue

Build a MoDMap from your dataset
Extend an existing MoDMap

Info

If you do not know the accession number of a species, you can search directly in NCBI from here. Samples you can try: [1] 62 mtDNA primates - [2] 112 mtDNA amphibia - [3] 39 HIV-1 genomes

Info

Extend a map by adding new points in a set of predefined MoDMaps. The new points can be given as comma separated accession numbers from NCBI. If you do not know the accession number of a species, you can search directly in NCBI from here.

Background map:
Extra Sequences:: Insert comma separated NCBI accession numbers
Load FASTA files

Settings of MoDMap selected

Show/Hide input data

Length of k-mers:
Get Taxonomy:
Number of groups:

Computation Results

Compute a distance

Compute approximated information distance (AID) between any pair of sequences, giving as input their NCBI accession numbers. AID distance has a value in [0,1]. If you do not know the accession number of a species, you can search directly in NCBI from here.

Settings

Samples you can try: [1] H.sapiens vs P.troglodytes - [2] H.sapiens vs H.neanderthalensis

Compute AID distance between (input NCBI accession numbers):

Summary

MoDMaps3D (Molecular Distance Maps 3D) is an alignment-free, fast, computationally lightweight webtool for computing and visualizing the relationships within a dataset of genomic DNA sequences, based on pairwise comparisons between their oligomer compositions. MoDMaps3D is a general-purpose interactive tool that can compute and display the interrelationships within any set of biological, simulated, or synthetic DNA sequences, closely related or completely unrelated, of the same length or of different lengths, several kbp-long or complete genomes.

Coded by:

Rallis Karamichalis, 2017

Github Code:

http://github.com/moleculardistancemaps/MoDMaps3D/

HotKeys:

Show/Hide full list

While on canvas:

A = Move camera Left
D = Move camera Right
W = Move camera Up
S = Move camera Down
E = Zoom camera In
Q = Zoom camera Out
Ctrl + LeftArrow = Rotate Left
Ctrl + UpArrow = Rotate Up
Ctrl + RightArrow = Rotate Right
Ctrl + DownArrow = Rotate Down
Left Mouse Click + Drag = Rotate to any direction

General Shortcuts:

Ctrl + F = Search field
Ctrl + Alt + R = Reset Camera view, keeping rotation
Ctrl + Alt + M = Toggle visibility of right menu
Ctrl + Alt + N = Toggle visibility of left menu