Difference between revisions of "S. cerevisiae Codon Usage Tables"
(Created page with "==These tables are from 1999 and were built using the known or predicted ORF sequences contained within the complete yeast genomic sequence.== *[http://downloads.yeastgenome.o...") |
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| − | == | + | == January 2011 Codon Usage (genome version 64-1-1) produced using EMBOSS cusp== |
| − | *[http:// | + | *[http://bun-dev.stanford.edu/unpublished_data/codon/64_1_1_all_nuclear.cusp 64_1_1_all_nuclear.cusp] for all ORFs (5865) encoded in the nuclear genome except the dubious ORFs and pseudogenes (i.e. including all verified, uncharacterized ORFs and transposable element genes without stop codons in them). |
| − | *[http:// | + | *[http://bun-dev.stanford.edu/unpublished_data/codon/64_1_1_dubious.cusp 64_1_1_dubious.cusp] for all nuclearly encoded dubious ORFs (801). |
| − | + | *[http://bun-dev.stanford.edu/unpublished_data/codon/64_1_1_mito.cusp 64_1_1_mito.cusp] for all mitochondrial non-dubious ORFs (19). | |
| − | == | + | == June 2008 Codon Usage (genome version 61-1-1) produced using GCG CodonFrequency== |
| + | All known or predicted ORF sequences contained within the complete yeast genomic sequence were included. | ||
| + | * [http://downloads.yeastgenome.org/unpublished_data/codon/s_cerevisiae-codonusage.txt s_cerevisiae-codonusage.txt] | ||
| + | |||
| + | ==January 1999 Codon Usage (genome version 12-1-1) produced using GCG CodonFrequency== | ||
| + | All known or predicted ORF sequences contained within the complete yeast genomic sequence were included. | ||
| + | *[http://downloads.yeastgenome.org/unpublished_data/codon/ysc.gene.cod ysc.gene.cod] from 3,222 ORFs assigned a gene name by the community as listed within SGD. | ||
| + | *[http://downloads.yeastgenome.org/unpublished_data/codon/ysc.orf.cod ysc.orf.cod] from 6,222 ORFs listed within SGD. | ||
| + | *[http://downloads.yeastgenome.org/unpublished_data/codon/yscmt.cod yscmt.cod] from 28 mitochondrion genes in [http://www.yeastgenome.org/reference/S000058438/overview Foury F, et al. (1998)] | ||
| + | |||
| + | ==1993 Codon Usage produced using GCG CodonFrequency== | ||
Duplicates, pseudogenes, mutant and synthetic genes were not included. Coding regions were specified using the Feature Table of each entry, then checked for accuracy. If more than one stop codon was found the sequence was not included. | Duplicates, pseudogenes, mutant and synthetic genes were not included. Coding regions were specified using the Feature Table of each entry, then checked for accuracy. If more than one stop codon was found the sequence was not included. | ||
| − | *[http://downloads.yeastgenome.org/unpublished_data/codon/ysc.g63.cod | + | *[http://downloads.yeastgenome.org/unpublished_data/codon/ysc.g63.cod ysc.g63.cod] from 435 genes found in GenBank 63 (March 1990). |
| − | |||
*[http://www.kazusa.or.jp/codon/ Codon Usage Database] from Yasukazu Nakamura using the latest GenBank Release. | *[http://www.kazusa.or.jp/codon/ Codon Usage Database] from Yasukazu Nakamura using the latest GenBank Release. | ||
Latest revision as of 08:34, 29 September 2014
Contents
January 2011 Codon Usage (genome version 64-1-1) produced using EMBOSS cusp
- 64_1_1_all_nuclear.cusp for all ORFs (5865) encoded in the nuclear genome except the dubious ORFs and pseudogenes (i.e. including all verified, uncharacterized ORFs and transposable element genes without stop codons in them).
- 64_1_1_dubious.cusp for all nuclearly encoded dubious ORFs (801).
- 64_1_1_mito.cusp for all mitochondrial non-dubious ORFs (19).
June 2008 Codon Usage (genome version 61-1-1) produced using GCG CodonFrequency
All known or predicted ORF sequences contained within the complete yeast genomic sequence were included.
January 1999 Codon Usage (genome version 12-1-1) produced using GCG CodonFrequency
All known or predicted ORF sequences contained within the complete yeast genomic sequence were included.
- ysc.gene.cod from 3,222 ORFs assigned a gene name by the community as listed within SGD.
- ysc.orf.cod from 6,222 ORFs listed within SGD.
- yscmt.cod from 28 mitochondrion genes in Foury F, et al. (1998)
1993 Codon Usage produced using GCG CodonFrequency
Duplicates, pseudogenes, mutant and synthetic genes were not included. Coding regions were specified using the Feature Table of each entry, then checked for accuracy. If more than one stop codon was found the sequence was not included.
- ysc.g63.cod from 435 genes found in GenBank 63 (March 1990).
- Codon Usage Database from Yasukazu Nakamura using the latest GenBank Release.
