Protocol

Full name SMRUCC.genomics.Analysis.SequenceTools.SequencePatterns.Motif.Protocol Assembly SMRUCC.genomics.Analysis.SequenceTools.SequencePatterns.MotifFinder Members 3

01 Syntax

SMRUCC.genomics.Analysis.SequenceTools.SequencePatterns.Motif.Protocol

02 Methods

Name	Overloads	Summary
PopulateMotifs	1	Motif motif finding workflow start from here
PWM	1	create PWM matrix of a motif model
Consensus	1	get consensus sequence of a pairwise alignment seed

03 Members

method PopulateMotifs #

PopulateMotifs(IEnumerable(Of FastaSeq), PopulatorParameter, Int32, Double, Boolean)

Motif motif finding workflow start from here

Parameters

Name	Type	Description
`inputs`	`IEnumerable(Of FastaSeq)`	-
`leastN%`	PopulatorParameter	-
`cleanMotif`	`Int32`	-
`param`	`Double`	-

method PWM #

PWM(MSAOutput, FastaSeq(), PopulatorParameter)

create PWM matrix of a motif model

Parameters

Name	Type	Description
`alignment`	`MSAOutput`	经过了多重序列比对之后，所有的成员的长度都已经是一致的了
`members`	`FastaSeq()`	-

method Consensus #

Consensus(HSP)

get consensus sequence of a pairwise alignment seed

Parameters

Name	Type	Description
`pairwise`	`HSP`	-