TMRNAGene

class pyaragorn.TMRNAGene(Gene)

A transfer-messenger RNA (tmRNA) gene.

Example

>>> rna_finder = pyaragorn.RNAFinder(11, trna=False, tmrna=True)
>>> tmrna = rna_finder.find_rna(str(record.seq))[0]
>>> tmrna.begin, tmrna.end
(198037, 198447)
>>> tmrna.peptide()
'AEKNEENFEMPAFMINNASAGANYMFA**'

orf(include_stop=True)

Retrieve the open-reading frame of the mRNA-like region.

Parameters:

include_stop (bool) – Whether or not to include the STOP codons in the returned nucleotide sequence. Defaults to True.

Returns:

str – The sequence of the mRNA-like region in the tmRNA gene, optionally without STOP codons.

peptide(include_stop=True)

Retrieve the peptide sequence of the mRNA-like region.

Parameters:

include_stop (bool) – Whether or not to include the STOP codons in the returned peptide sequence. Defaults to True.

Returns:

str – The translation of the mRNA-like region of the tmRNA gene, optionally without STOP codons.

sequence()

Retrieve the full sequence of the RNA gene.

begin

The sequence coordinate at which the gene begins.

Hint

This coordinate is 1-based, inclusive. To use it to index a Python array or string, subtract one.

Type:

int

end

The sequence coordinate at which the gene end.

Hint

This coordinate is 1-based, inclusive. To use it to index a Python array or string, subtract one.

Type:

int

energy

The approximated normalised energy of the RNA structure.

Type:

float

length

The length of the RNA gene.

Type:

int

orf_length

The length of the open-reading frame (in nucleotides).

Type:

int

orf_offset

The offset in the gene at which the open-reading frame starts.

Type:

int

permuted

Whether this tmRNA gene is a permuted gene.

Type:

bool

raw_energy

The un-normalized energy value of the RNA structure.

Type:

float

strand

-1 if the gene is on the reverse strand, +1 otherwise.

Type:

int