GaryGaulin
Posts: 5385 Joined: Oct. 2012
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Quote (N.Wells @ Nov. 20 2016,03:04) | Progress of a sort, thank you. What do you mean by "each horizontal band line along the chromosome"? Why do you want each possible triplet? Alternative splicing happens, but not every possible triple gets used, and indeed much of the chromosome goes entirely uncoded. Once you have that data, how does your program display it? |
More info:
Quote | This program digitally bands chromosomes according to the abundance of (4^3) 64 possible three letter DNA sequences:
AAA,AAC,AAG,AAT, ACA,ACC,ACG,ACT, AGA,AGC,AGG,AGT, ATA,ATC,ATG,ATT, CAA,CAC,CAG,CAT, CCA,CCC,CCG,CCT, CGA,CGC,CGG,CGT, CTA,CTC,CTG,CTT, GAA,GAC,GAG,GAT, GCA,GCC,GCG,GCT, GGA,GGC,GGG,GGT, GTA,GTC,GTG,GTT, TAA,TAC,TAG,TAT, TCA,TCC,TCG,TCT, TGA,TGC,TGG,TGT, TTA,TTC,TTG,TTT
For each selected Assembly (such as Human_, Bonobo_) found in the DNA folder: the program scans through Fasta format files one (A,C,G,T) base location at a time, while counting how many times each of the 64 triplets occur in each of the one pixel wide vertical band lines shown along the horizontal length of the chromosome. A "Bases per Band" scrollbar controls how many base pairs each band line represents.
A "Brightness" control is provided for adjusting how brightly the abundances are displayed in the illustration. To better show banding of low abundance sequences there is an optional "Brightness Adjust" checkbox for making each of the 32 horizontal groups the same brightness, regardless of overall abundances.
When comparing with our closest descendents our fused Chromosome 2 has a corresponding part A that is shown in the above left, while part B is shown below right of the fused chromosome. |
The method used to find the strings is very fast but only works for a string length of 3 and is not easy to figure out, and work with. There is already a step where it scans through the entire fasta file anyway and it would seem to simplify things by taking the chromosome one pixel worth of bases (instead of line of pixels all the same color) at a time then show folded up with an up and down accordion fold, or in fragments all going the same way. The "bands" will then also have a signature texture.
-------------- The theory of intelligent design holds that certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection.
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