ProfileHMM {SMRUCC.genomics.Analysis.SequenceTools.HMMER}

.NET clr documentation

ProfileHMM

Description

Profile HMM模型类 表示HMMER3格式的隐马尔可夫模型

Profile HMM是一种特殊的隐马尔可夫模型，专门用于蛋白质序列比对。 它包含三种状态：

• Match (M): 匹配状态，对应模型中的一个保守位置

• Insert (I): 插入状态，允许在模型位置之间插入残基

• Delete (D): 删除状态，允许跳过模型中的某个位置

每个位置有：

• 20个氨基酸的匹配发射概率

• 20个氨基酸的插入发射概率

• 7个转移概率

Declare

            
# namespace SMRUCC.genomics.Analysis.SequenceTools.HMMER
export class ProfileHMM {
   Alphabet: string;
   Checksum: integer;
   CompositionEmission: double;
   CompositionInsert: double;
   CompositionTransitions: double;
   EffectiveNum: double;
   HMMInitialProb: double;
   HMMObservables: Observable[];
   HMMStates: StatesObject[];
   InsertEmissions: iterates(Double[]);
   Length: integer;
   MatchEmissions: iterates(Double[]);
   Name: string;
   NumSequences: integer;
   StatsForward: tuple[double, double];
   StatsMSV: tuple[double, double];
   StatsViterbi: tuple[double, double];
   Transitions: iterates(Double[]);
   Version: string;
}

        

.NET clr type reference tree

1. use by property member HMMObservables: Observable
2. use by property member HMMStates: StatesObject
3. use by property member InsertEmissions: iterates(Double)
4. use by property member MatchEmissions: iterates(Double)
5. use by property member StatsForward: tuple[double, double]
6. use by property member StatsMSV: tuple[double, double]
7. use by property member StatsViterbi: tuple[double, double]
8. use by property member Transitions: iterates(Double)

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