\Amelaye\BioPHP\Domain\Sequence\TraitsSequenceTrait

Trait SequenceTrait

Summary

Methods
Properties
Constants
compDNA()
compRNA()
revCompDNA()
revCompRNA()
cleanSequence()
No public properties found
No constants found
No protected methods found
No protected properties found
N/A
No private methods found
No private properties found
N/A

Methods

compDNA()

compDNA(string  $sSequence) : string

Returns complement of sequence $sSequence

Parameters

string $sSequence

Throws

\Exception

Returns

string

compRNA()

compRNA(string  $sSequence) : string

Returns complement of RNA sequence

Parameters

string $sSequence

Throws

\Exception

Returns

string

revCompDNA()

revCompDNA(string  $sSequence) : string

Will yield the Reverse complement of a DNA sequence. Allows degenerated nucleotides

Parameters

string $sSequence

is the sequence

Throws

\Exception

Returns

string

revCompRNA()

revCompRNA(string  $sSequence) : string

Will yield the Reverse complement of a RNA sequence. Allows degenerated nucleotides

Parameters

string $sSequence

is the sequence

Throws

\Exception

Returns

string

cleanSequence()

cleanSequence( $sSequence,  $sMolType) : bool

Check if characters outside our 20-letter amino alphabet is included in the sequence.

If there are unknown characters, then do not compute molwt and instead return FALSE.

Parameters

$sSequence
$sMolType

Returns

bool