AminoSee DNA Render Summary for Caenorhabditis_elegans.WBcel235.dna_sm.toplevel.fa

Caenorhabditisel.dna_sm.toplevel


1D Linear Map Image

2D Hilbert Map Image

Render Summary

    
    Canonical this.justNameOfDNA: Caenorhabditisel.dna_sm.toplevel
    Source: Caenorhabditis_elegans.WBcel235.dna_sm.toplevel.fa
    Full path: /home/tom/Sites/AminoSee/dna/Caenorhabditis_elegans.WBcel235.dna_sm.toplevel.fa
    Started: 10:40:09 pm Finished: 10:41:38 pm Used: 1 minute, 28.983 seconds  
    Machine load averages: 5.52 / 5.02 / 13.68
    DNA Input bytes: 97.23MB 1.07MB/sec
    Image Output bytes: 261.16KB
    Pixels (linear): 66,857 Image aspect Ratio: fix
    Pixels (hilbert): 4,096 (auto)
    Custom flags: -UC_500-------M3 C500 "Science mode" render style
    Estimated Codons: 33,986,093 (filesize % 3)
    Actual Codons matched: 33,428,799  
    Estimate accuracy: 102% of actual 
    Non-coding characters: 401
    Coding characters: 100,286,841
    Codons per pixel: 500 (linear) 8,161.25 (hilbert projection)
    Linear to Hilbert reduction: 16.32 Oversampling: 8
    Amino acid blend opacity: 0.2%
    Max pix setting: 8,000,000
    3th Hilbert curve infintite recursion dimension
    Darken Factor 1 / Highlight Factor 16.51
    Gigabytes processed on this profile: 487.835 Run ID: 1564221458 5931th run on cheese
    Total renders: undefined Project opens: 151 (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

33428799 n/a AminoSee Reference Hilbert Image Caenorhabditisel.dna_sm.toplevel Reference Linear Image Caenorhabditisel.dna_sm.toplevel
Reference

255,128,128

0 Composite of all amino acids Caenorhabditisel.dna_sm.toplevel Reference Caenorhabditisel.dna_sm.toplevel Reference
Amber

47°

255,227,128

350,727 STOP Codon Caenorhabditisel.dna_sm.toplevel Amber Caenorhabditisel.dna_sm.toplevel Amber
Tryptophan

188°

128,238,255

411,280 Group I: Nonpolar amino acids Caenorhabditisel.dna_sm.toplevel Tryptophan Caenorhabditisel.dna_sm.toplevel Tryptophan
Methionine

110°

149,255,128

528,326 START Codon Caenorhabditisel.dna_sm.toplevel Methionine Caenorhabditisel.dna_sm.toplevel Methionine
Opal

240°

128,128,255

707,395 STOP Codon Caenorhabditisel.dna_sm.toplevel Opal Caenorhabditisel.dna_sm.toplevel Opal
Ochre

255,128,128

728,847 STOP Codon Caenorhabditisel.dna_sm.toplevel Ochre Caenorhabditisel.dna_sm.toplevel Ochre
Aspartic acid

31°

255,193,128

802,003 Group III: Acidic amino acids Caenorhabditisel.dna_sm.toplevel Aspartic acid Caenorhabditisel.dna_sm.toplevel Aspartic acid
Histidine

329°

255,128,193

881,787 Group IV: Basic amino acids Caenorhabditisel.dna_sm.toplevel Histidine Caenorhabditisel.dna_sm.toplevel Histidine
Cysteine

63°

249,255,128

947,314 Group II: Polar, uncharged amino acids Caenorhabditisel.dna_sm.toplevel Cysteine Caenorhabditisel.dna_sm.toplevel Cysteine
Tyrosine

282°

217,128,255

1,040,068 Group II: Polar, uncharged amino acids Caenorhabditisel.dna_sm.toplevel Tyrosine Caenorhabditisel.dna_sm.toplevel Tyrosine
Glycine

78°

217,255,128

1,116,059 Group I: Nonpolar amino acids Caenorhabditisel.dna_sm.toplevel Glycine Caenorhabditisel.dna_sm.toplevel Glycine
Alanine

94°

183,255,128

1,116,319 Group I: Nonpolar amino acids Caenorhabditisel.dna_sm.toplevel Alanine Caenorhabditisel.dna_sm.toplevel Alanine
Proline

344°

255,128,162

1,123,517 Group I: Nonpolar amino acids Caenorhabditisel.dna_sm.toplevel Proline Caenorhabditisel.dna_sm.toplevel Proline
Glutamine

250°

149,128,255

1,185,774 Group II: Polar, uncharged amino acids Caenorhabditisel.dna_sm.toplevel Glutamine Caenorhabditisel.dna_sm.toplevel Glutamine
Glutamic acid

16°

255,162,128

1,278,808 Group III: Acidic amino acids Caenorhabditisel.dna_sm.toplevel Glutamic acid Caenorhabditisel.dna_sm.toplevel Glutamic acid
Valine

125°

128,255,138

1,613,654 Group I: Nonpolar amino acids Caenorhabditisel.dna_sm.toplevel Valine Caenorhabditisel.dna_sm.toplevel Valine
Threonine

219°

128,172,255

1,615,660 Group II: Polar, uncharged amino acids Caenorhabditisel.dna_sm.toplevel Threonine Caenorhabditisel.dna_sm.toplevel Threonine
Asparagine

266°

183,128,255

1,850,991 Group II: Polar, uncharged amino acids Caenorhabditisel.dna_sm.toplevel Asparagine Caenorhabditisel.dna_sm.toplevel Asparagine
Arginine

297°

249,128,255

1,920,505 Group IV: Basic amino acids Caenorhabditisel.dna_sm.toplevel Arginine Caenorhabditisel.dna_sm.toplevel Arginine
Isoleucine

157°

128,255,206

2,430,383 Group I: Nonpolar amino acids Caenorhabditisel.dna_sm.toplevel Isoleucine Caenorhabditisel.dna_sm.toplevel Isoleucine
Lysine

313°

255,128,227

2,672,335 Group IV: Basic amino acids Caenorhabditisel.dna_sm.toplevel Lysine Caenorhabditisel.dna_sm.toplevel Lysine
Serine

203°

128,206,255

2,893,966 Group II: Polar, uncharged amino acids Caenorhabditisel.dna_sm.toplevel Serine Caenorhabditisel.dna_sm.toplevel Serine
Phenylalanine

172°

128,255,238

2,986,319 Group I: Nonpolar amino acids Caenorhabditisel.dna_sm.toplevel Phenylalanine Caenorhabditisel.dna_sm.toplevel Phenylalanine
Leucine

141°

128,255,172

3,226,761 Group I: Nonpolar amino acids Caenorhabditisel.dna_sm.toplevel Leucine Caenorhabditisel.dna_sm.toplevel 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: