MoDMaps3D - Main Menu

Welcome to MoDMaps3D!

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):

For kmer size:

Coded by:

Rallis Karamichalis, 2016

Github Code:

http://github.com/rallis/MoDMaps3D/

HotKeys:

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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