bioseq.config

class bioseq.config.AlignmentConfig[source]

Align parameters

MATCH

score when meet a match pair

Type: float

MISMATCH

score when meet a mismatch pair

Type: float

GAP_OPEN

score when open a gap

Type: float

GAP_EXTEND

score when extend a gap

Type: float

bioseq.config.CODON_TABLE: Dict[str, str]

mRNA codon table, used to transcript()

Type: meta hide-value

bioseq.config.HYDROPATHY

Hydrophobicity of 20 amino acids, the higher, the more hydrophobic
Author(s): Kyte J., Doolittle R.F.
Reference: J. Mol. Biol. 157:105-132(1982).

Type: meta hide-value

bioseq.config.MW: Dict

Molecular weight table, include “Peptide”, “DNA”, “RNA”.

reference https://www.thermofisher.cn/cn/zh/home/references/ambion-tech-support/rna-tools-and-calculators/dna-and-rna-molecular-weights-and-conversions.html

Type: meta hide-value

bioseq.config.NC_INFO: Dict

Complementary table of nucleic acid, include “DNA_COMPLEMENT”, “RNA_COMPLEMENT”.

Type: meta hide-value

bioseq.config.PK

pK value of charged amino acids.

reference biopython.SeqUtils.IsoelectricPoint, Value from EMBOSS Database

Type: meta hide-value

bioseq.config.START_CODON: List[str]

Start code list, default is [“AUG”], used to get_orf().
All codon in this list will be set to start of ORF.
When from bioseq.utils import START_CODON, to change a start codon, don’t assign to START_CODON, use START_CODON[0] = "ATT" to instead.

Type: meta hide-value

bioseq.config.SYMBOL: Dict[str, List[str]]

SYMBOL[“printAlign”] - Use to print alignment sequences

Type: meta hide-value