AminoSee DNA Render Summary for Brown_Kiwi_NW_013982187v1.fa

Brown_Kiwi_NW_013982187v1


1D Linear Map Image

2D Hilbert Map Image

Render Summary

    
    Canonical this.justNameOfDNA: Brown_Kiwi_NW_013982187v1
    Source: Brown_Kiwi_NW_013982187v1.fa
    Full path: /home/tom/Sites/AminoSee/dna/Brown_Kiwi_NW_013982187v1.fa
    Started: 10:10:33 pm Finished: 10:39:48 pm Used: 29 minutes, 13.313 seconds  
    Machine load averages: 3.69 / 5.08 / 14.8
    DNA Input bytes: 1.45GB 853.52KB/sec
    Image Output bytes: 3.2MB
    Pixels (linear): 839,048 Image aspect Ratio: fix
    Pixels (hilbert): 65,536 (auto)
    Custom flags: -UC_500-------M5 C500 "Science mode" render style
    Estimated Codons: 518,291,295 (filesize % 3)
    Actual Codons matched: 419,524,426  
    Estimate accuracy: 124% of actual 
    Non-coding characters: 217,626,006
    Coding characters: 1,532,925,470
    Codons per pixel: 500 (linear) 6,401.43 (hilbert projection)
    Linear to Hilbert reduction: 12.8 Oversampling: 8
    Amino acid blend opacity: 0.2%
    Max pix setting: 8,000,000
    5th Hilbert curve infintite recursion dimension
    Darken Factor 1 / Highlight Factor 16.51
    Gigabytes processed on this profile: 487.72 Run ID: 1564221458 5929th run on cheese
    Total renders: undefined Project opens: 149 (only increments when using --image --help --html or --explorer)
    AminoSee version: 1.19.3
    

AminoSeeNoEvil

DNA/RNA Chromosome Viewer

A new way to view DNA that attributes a colour hue to each Amino acid codon this.triplet



http://localhost:4321/aminosee/output/50KB_TestPattern/50KB_TestPattern.txt_linear__Reference_c1_sci.png
Amino Acid Hue° RGB Count Description Hilbert PNG Linear PNG
All amino acids combined =

n/a

n/a

419524426 n/a AminoSee Reference Hilbert Image Brown_Kiwi_NW_013982187v1 Reference Linear Image Brown_Kiwi_NW_013982187v1
Reference

255,128,128

0 Composite of all amino acids Brown_Kiwi_NW_013982187v1 Reference Brown_Kiwi_NW_013982187v1 Reference
Amber

47°

255,227,128

5,215,637 STOP Codon Brown_Kiwi_NW_013982187v1 Amber Brown_Kiwi_NW_013982187v1 Amber
Tryptophan

188°

128,238,255

6,653,154 Group I: Nonpolar amino acids Brown_Kiwi_NW_013982187v1 Tryptophan Brown_Kiwi_NW_013982187v1 Tryptophan
Methionine

110°

149,255,128

7,538,596 START Codon Brown_Kiwi_NW_013982187v1 Methionine Brown_Kiwi_NW_013982187v1 Methionine
Opal

240°

128,128,255

8,073,922 STOP Codon Brown_Kiwi_NW_013982187v1 Opal Brown_Kiwi_NW_013982187v1 Opal
Ochre

255,128,128

8,536,988 STOP Codon Brown_Kiwi_NW_013982187v1 Ochre Brown_Kiwi_NW_013982187v1 Ochre
Aspartic acid

31°

255,193,128

9,490,258 Group III: Acidic amino acids Brown_Kiwi_NW_013982187v1 Aspartic acid Brown_Kiwi_NW_013982187v1 Aspartic acid
Tyrosine

282°

217,128,255

12,588,615 Group II: Polar, uncharged amino acids Brown_Kiwi_NW_013982187v1 Tyrosine Brown_Kiwi_NW_013982187v1 Tyrosine
Histidine

329°

255,128,193

13,513,605 Group IV: Basic amino acids Brown_Kiwi_NW_013982187v1 Histidine Brown_Kiwi_NW_013982187v1 Histidine
Glutamic acid

16°

255,162,128

15,156,384 Group III: Acidic amino acids Brown_Kiwi_NW_013982187v1 Glutamic acid Brown_Kiwi_NW_013982187v1 Glutamic acid
Asparagine

266°

183,128,255

16,143,922 Group II: Polar, uncharged amino acids Brown_Kiwi_NW_013982187v1 Asparagine Brown_Kiwi_NW_013982187v1 Asparagine
Cysteine

63°

249,255,128

16,443,155 Group II: Polar, uncharged amino acids Brown_Kiwi_NW_013982187v1 Cysteine Brown_Kiwi_NW_013982187v1 Cysteine
Glutamine

250°

149,128,255

17,678,881 Group II: Polar, uncharged amino acids Brown_Kiwi_NW_013982187v1 Glutamine Brown_Kiwi_NW_013982187v1 Glutamine
Proline

344°

255,128,162

19,930,029 Group I: Nonpolar amino acids Brown_Kiwi_NW_013982187v1 Proline Brown_Kiwi_NW_013982187v1 Proline
Glycine

78°

217,255,128

19,932,793 Group I: Nonpolar amino acids Brown_Kiwi_NW_013982187v1 Glycine Brown_Kiwi_NW_013982187v1 Glycine
Alanine

94°

183,255,128

20,581,787 Group I: Nonpolar amino acids Brown_Kiwi_NW_013982187v1 Alanine Brown_Kiwi_NW_013982187v1 Alanine
Arginine

297°

249,128,255

21,251,126 Group IV: Basic amino acids Brown_Kiwi_NW_013982187v1 Arginine Brown_Kiwi_NW_013982187v1 Arginine
Threonine

219°

128,172,255

21,418,611 Group II: Polar, uncharged amino acids Brown_Kiwi_NW_013982187v1 Threonine Brown_Kiwi_NW_013982187v1 Threonine
Valine

125°

128,255,138

21,423,289 Group I: Nonpolar amino acids Brown_Kiwi_NW_013982187v1 Valine Brown_Kiwi_NW_013982187v1 Valine
Isoleucine

157°

128,255,206

22,761,560 Group I: Nonpolar amino acids Brown_Kiwi_NW_013982187v1 Isoleucine Brown_Kiwi_NW_013982187v1 Isoleucine
Phenylalanine

172°

128,255,238

24,480,694 Group I: Nonpolar amino acids Brown_Kiwi_NW_013982187v1 Phenylalanine Brown_Kiwi_NW_013982187v1 Phenylalanine
Lysine

313°

255,128,227

24,911,380 Group IV: Basic amino acids Brown_Kiwi_NW_013982187v1 Lysine Brown_Kiwi_NW_013982187v1 Lysine
Serine

203°

128,206,255

38,866,347 Group II: Polar, uncharged amino acids Brown_Kiwi_NW_013982187v1 Serine Brown_Kiwi_NW_013982187v1 Serine
Leucine

141°

128,255,172

46,933,692 Group I: Nonpolar amino acids Brown_Kiwi_NW_013982187v1 Leucine Brown_Kiwi_NW_013982187v1 Leucine
19 Amino Acids, 4 Start/Stop codes, 1 NNN . . . .

About Start and Stop Codons

The codon AUG is called the START codon as it the first codon in the transcribed mRNA that undergoes translation. AUG is the most common START codon and it codes for the amino acid methionine (Met) in eukaryotes and formyl methionine (fMet) in prokaryotes. During protein synthesis, the tRNA recognizes the START codon AUG with the help of some initiation factors and starts translation of mRNA. Some alternative START codons are found in both eukaryotes and prokaryotes. Alternate codons usually code for amino acids other than methionine, but when they act as START codons they code for Met due to the use of a separate initiator tRNA. Non-AUG START codons are rarely found in eukaryotic genomes. Apart from the usual Met codon, mammalian cells can also START translation with the amino acid leucine with the help of a leucyl-tRNA decoding the CUG codon. Mitochondrial genomes use AUA and AUU in humans and GUG and UUG in prokaryotes as alternate START codons. In prokaryotes, E. coli is found to use AUG 83%, GUG 14%, and UUG 3% as START codons. The lacA and lacI coding this.regions in the E coli lac operon don’t have AUG START codon and instead use UUG and GUG as initiation codons respectively.

Linear Projection

The following image is in raster order, top left to bottom right: