In order to enable users of the Visual Genome Browser to share their findings, I have now added what I called a "long non-coding DNA Cube" (lnCubeDNA).
It represents a shortcut which can be shared between users that "carries" all of the genome browser parameters to download the same genome and JUMP to the correct genome location and show the "discovery" to the other user.
A Cube DNA for the display of the centromeric region on chromosome 7 looks as follows:
GTAACCTCTTTTTTTTTTT
TGGGAATTCCCTCTTTTTC
GGATAGTTATTTTTTTTTT
TTTTTTTTTTTTTCTTTTT
GATGGTGTCTATTGCGAGC
AGCTTTGTGCTAAGTAATA
GTCATCCTACGTGATAATT
GTAAGGGAAGTTGATACGC
TCACATCATCACATTTATT
TATTGCATCTCCCATATCA
TACATTTCCTTTTGGTACC
CAAACACTCACTCATTCAC
ACAGTCACACACTCATGAA
GGTTATCATTGATATCTAT
TCTGAAGCATCTTGGGTGA
GTAGGTGGGTAGTAGGGTG
TCATTTTTACTGGGCGAGG
GGCAGCATATTTTTTTTTT
TTAAAAAAAAAGAGGTTAC
It is called a Cube (or lnCube) because it has exactly the same number of columns as rows
and it also resembles a Type-2 DNA Transposon (jumping gene) of which the start and end DNA "repeat" is the reverse complement of each other. The terminal inverted repeats of jumping genes are the DNA sequences to which transposase proteins bind in order to recognise the location of the transposon in the genome.
GTAACCTCTTTTTTTTT
CATTGGAGAAAAAAAAA
When you share this DNA string with another user his genome browser will JUMP to the location of the shortcut "Cube" which was shared with you by the other user to allow him to "see what they saw".
Anybody can try out this cube in the Visual Genome Browser. The cube points to location:
chr7:60236243-60236243
in the HG38 human genome.
The result will point to a location within the Long Satellite repeats of the centromeric region.
The width of the Zoomed DNA view is changed to 170 nucleotides.
Interesting to know that this 170 also corresponds to the number of bases from nucleosome to nucleosome which are used to package the DNA in the heterochromatin of the human genome, so it makes sense that the repeats show up at intervals of 170 nucleotides/bases.
When one generates a Dot-Plot, the repeats actually show up as 340 bases with minor lines at 170 bases, and much sharper lines at 6 x 170 = 1022
The Cube for the 1022 display is:
GTAACATGTTTTTTTTTTTTG
GGAATTCCATGTTTTTCGGAT
AGTTATTTTTTTTTTTTTTTT
TTTTTTTCTTTTTGATGGTGT
CTATTGCGAGCAGCTTTGTGC
TAAGTAATAGTCATCCTACGT
GATAATTGTAAGGGAAGTTGA
TACGCTCACATCATCACATTT
GTTTATTTGATCTCGGACATC
ACATCCTTTTGGTACCCAAAC
ACTCACTCATTCACACAGTCA
CACACTCATGAAGGTTATCAT
TGATATCTATCCCTTGACGTT
CGCACGCACGCACGCTCGCTC
GCGCGCTCGCCTTGGCGTACG
CCTTGATTTTGGTCGCGCTCG
TTCATTCAGGCAGCTTAGGTG
AGTAGGTGGGTGGTATGGTTT
CATTTTCCGATTAAACCTTGC
CCGCCTTTTTTTTTTTTTTCC
CAAAAAAAAAAAACATGTTAC
So, in short, you can use the "jumping genes" I created to share findings between instances of the Genome Browser.
