Data Set Information:

我们检查了CUTG数据库中不同分类群的大量不同生物样本的基因组编码DNA中的密码子使用频率，通过将CUTG的细菌（bct）重新分类为古细菌（arc）、质粒（plm）和固有细菌，我们进一步手动管理和协调这些现有条目（与原始标签“bct”保持一致。通过从文件“qbxxx.spsum.txt”（其中xxx=bct（细菌）、inv（无脊椎动物）、mam（哺乳动物）、pln（植物）、pri（灵长类动物）、rod（啮齿动物）、vrt（脊椎动物））中提取，简化了原始“bct”域的重新分类记录不同的属名称，并按属进行分类。共有514个不同的属名称。检查不同的属类别，并在适当情况下重新标记为“arc”。在真细菌记录中，区分了细菌基因组本身（与原始标签“bct”保持一致）和细菌质粒（现在标记为“plm”）。

按照这些预处理步骤，最终的数据集文件将CUTG数据库qbxxx.spsum.txt的所有条目包含在一个文本文件中。如上所述，qbbct.spsum.txt条目被分离为“bct”（即真细菌）、“plm”（质粒）和“arc”（古细菌），这是CUTG数据库中最初没有做的区分。

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 '@' uchicago.edu