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CUTG数据库 不同生物样本的基因组编码DNA中的密码子使用频率数据

CUTG数据库 不同生物样本的基因组编码DNA中的密码子使用频率数据



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Data Preview ? 1.92M

    Data Structure ?


    Data Set Information:



    Attribute Information:

    Column 1: Kingdom
    Column 2: DNAtype
    Column 3: SpeciesID
    Column 4: Ncodons
    Column 5: SpeciesName
    Columns 6-69: codon (header: nucleotide bases; entries: frequency of usage (5 digit floating point number))

    The 'Kingdom' is a 3-letter code corresponding to `xxx' in the CUTG database name: 'arc'(archaea), 'bct'(bacteria), 'phg'(bacteriophage), 'plm' (plasmid), 'pln' (plant), 'inv' (invertebrate), 'vrt' (vertebrate), 'mam' (mammal), 'rod' (rodent), 'pri' (primate), and 'vrl'(virus) sequence entries.  Note that the CUTG database does not contain 'arc' and 'plm' (these have been manually curated ourselves).

    The 'DNAtype' is denoted as an integer for the genomic composition in the species: 0-genomic, 1-mitochondrial, 2-chloroplast, 3-cyanelle, 4-plastid, 5-nucleomorph, 6-secondary_endosymbiont, 7-chromoplast, 8-leucoplast, 9-NA, 10-proplastid, 11-apicoplast, and 12-kinetoplast.

    The species identifier ('SpeciesID') is an integer, which uniquely indicates the entries of an organism. It is an accession identifier for each different species in the original CUTG database, followed by the first item listed in each genome.

    The number of codons (`Ncodons') is the algebraic sum of the numbers listed for the different codons in an entry of CUTG. Codon frequencies are normalized to the total codon count, hence the number of occurrences divided by 'Ncodons' is the codon frequencies listed in the data file.

    The species' name ('SpeciesName') is represented in strings purged of `comma' (which are now replaced by `space'). This is a descriptive label of the name of the species for data interpretations.

    Lastly, the codon frequencies ('codon') including 'UUU', 'UUA', 'UUG', 'CUU', etc., are recorded as floats (with decimals in 5 digits).

    Relevant Papers:

    Khomtchouk BB, Liang Y, Nonner WF: 'Codon usage bias levels predict taxonomic identity and genetic composition'.  bioRxiv, 2020.

    Citation Request:

    Khomtchouk BB, Liang Y, Nonner WF: 'Codon usage bias levels predict taxonomic identity and genetic composition'.  bioRxiv, 2020.  

    Nakamura Y, Gojobori T, Ikemura T: 'Codon usage tabulated from international DNA sequence databases: status for the year 2000'.  Nucleic Acids Research, 2000, 28:292.

    Bohdan Khomtchouk, Ph.D.  University of Chicago, Department of Medicine, Section of Computational Biomedicine and Biomedical Data Science.  Email: bohdan '@'