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Analyser
The package is designed for analyzing the data. This is documentation for analyzer package. Functions for general use:
Functions for advanced use:
Detailed description of functions are given below.
Calculates rscu values for each codon. It is inspired by the works of Sharp and Li (1987). For details click here.
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records: The generator object containing sequence object -
genetic_code_num: Genetic table number for codon table (click here for details) -
min_len_threshold: Minimum length of nucleotide sequence to be considered as gene (Default 200) -
gene_analysis: Option if gene analysis (True) or genome analysis (False) (Default false)
The function returns dictionary containing codon and rscu value pairs, if gene_analysis is false. Else will return the
dictionary containing gene name and the dictionary which contains codon and rscu value pairs.
Calculates codon adaptation index values for each codon. It is inspired by the works of Sharp and Li (1987). For details click here.
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records: The generator object containing sequence object -
genetic_code_num: Genetic table number for codon table (click here for details) -
min_len_threshold: Minimum length of nucleotide sequence to be considered as gene (Default 200) -
gene_analysis: Option if gene analysis (True) or genome analysis (False) (Default false)
The function returns dictionary containing codon and cai value pairs, if gene_analysis is false. Else will return the
dictionary containing gene name and the dictionary which contains codon and cai value pairs.
Calculates codon bias index values for each amino acid. It is inspired by the works of Bennetzen and Hall (1982). For details click here.
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records: The generator object containing sequence object -
genetic_code_num: Genetic table number for codon table (click here for details) -
min_len_threshold: Minimum length of nucleotide sequence to be considered as gene (Default 200) -
gene_analysis: Option if gene analysis (True) or genome analysis (False) (Default false)
The function returns dictionary containing amino acid and cbi value, optimal codon pairs, if gene_analysis is false.
Else it will return the dictionary containing gene name and the dictionary which contains amino acid and cbi value,
optimal codon pairs.
Calculates effective number of codons value for a given sequences. It is inspired by the works of Wright (1989). For details click here. Some revisions to the original method have been done for certain classes of protein based on the works of Fuglsang (2004). For details click here.
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records: The generator object containing sequence object -
genetic_code_num: Genetic table number for codon table (click here for details) -
min_len_threshold: Minimum length of nucleotide sequence to be considered as gene (Default 200) -
gene_analysis: Option if gene analysis (True) or genome analysis (False) (Default false)
The function returns the effective number of codons value for given sequence if gene_analysis is false. Else it will
return a dictionary containing gene number and corresponding ENc value
Calculates percentage of G content for third position
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seq: Provided sequence
Returns the percentage of G content for third position
Calculates percentage of A content for third position
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seq: Provided sequence
Returns the percentage of A content for third position
Calculate G+C content: total, for first, second and third positions
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seq: Provided sequence
Returns the G+C percentage for the entire sequence, and the three codon positions
Calculate A+T content: total, for first, second and third positions
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seq: Provided sequence
Returns the A+T percentage for the entire sequence, and the three codon positions
Filters the list of reference based on given threshold of length
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records: A generator object holding the sequence objects -
min_len_threshold: Minimum length of nucleotide sequence to be considered as gene
Returns the list of usable sequences
Creates the protein, codon dictionary where protein is key
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codon_table: The codon table
Returns the dictionary of protein, codon pair having protein as key
Creates the sf value and protein dictionary where sf value is key
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codon_table: The codon table
Returns the dictionary of sf value and protein dictionary where sf value is key
Calculates codon bias index (CBI) for a given protein seq based on Bennetzen and Hall (1982). For details click here.
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prot_seq: The Amino Acid -
reference: List of reference nucleotide sequences -
genetic_code: Genetic table number for codon table (click here for details)
This function may raise the following warnings
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NoSynonymousCodonWarning: When there is no synonymous codons -
MissingCodonWarning: When no codons translate to provided Amino acid
Returns a tuple of CBI vals and the optimal codons
Calculates Effective number of codons (Enc) for a given list of sequences based on Wright (1989) (click here) and Fuglsang (2004) (click here).
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references: List of reference nucleotide sequences -
genetic_code: Genetic table number for codon table
This function may raise the following warnings and errors
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MissingCodonWarning: When no codons translate to provided Amino acid -
NoProteinError: If there is no codon for a certain set of amino acid
Returns calculated Enc value for the sequence(s)
- Bennetzen, J.L. and Hall, B.D. (1982) “Codon selection in yeast.,” Journal of Biological Chemistry, 257(6), pp. 3026–3031. Available at: https://doi.org/10.1016/s0021-9258(19)81068-2
- Fuglsang, A. (2004) “The ‘effective number of codons’ revisited,” Biochemical and Biophysical Research Communications, 317(3), pp. 957–964. Available at: https://doi.org/10.1016/j.bbrc.2004.03.138
- Sharp, P.M. and Li, W.-H. (1987) “The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications,” Nucleic Acids Research, 15(3), pp. 1281–1295. Available at: https://doi.org/10.1093/nar/15.3.1281
- Wright, F. (1990) “The ‘effective number of codons’ used in a gene,” Gene, 87(1), pp. 23–29. Available at: https://doi.org/10.1016/0378-1119(90)90491-9.
© 2023 Souradipto Choudhuri
© 2023 Souradipto Choudhuri