Create or edit hidden Markov model (HMM) profile structure

* Model* = hmmprofstruct(

`Length`

`Model`

`Length`

`Field1`

`Field1Value`

`Field2`

`Field2Value`

`NewModel`

`Model`

`Field1`

`Field1Value`

`Field2`

`Field2Value`

`Length` | Number of match states in the model. |

`Model` | MATLAB^{®} structure containing fields for the parameters
of an HMM profile created with the `hmmprofstruct` function. |

`Field` | Character vector containing a field name in the structure .
See the table below for field names.`Model` |

`FieldValue` | Value associated with . See
the table below for descriptions.`Field` |

`Model` | MATLAB structure containing fields for the parameters of an HMM profile. |

returns * Model* = hmmprofstruct(

`Length`

`Model`

`Length`

returns an HMM profile structure using the specified
parameters. All other required parameters are set to default values.* Model* = hmmprofstruct(

`Length`

`Field1`

`Field1Value`

`Field2`

`Field2Value`

returns an updated HMM profile structure using the
specified parameters. All other parameters are taken from the input * NewModel* = hmmprofstruct(

`Model`

`Field1`

`Field1Value`

`Field2`

`Field2Value`

`Model`

The MATLAB structure * Model* contains
the following fields, which are the required and optional parameters
of an HMM profile. All probability values are in the [0 1] range.

Field | Description | ||
---|---|---|---|

`ModelLength` | Integer specifying the length of the profile (number of MATCH states). | ||

`Alphabet` | Character vector specifying the alphabet used in the model.
Choices are `'AA'` (default) or `'NT'` .
| ||

`MatchEmission` | Symbol emission probabilities in the MATCH states. Either of the following: | ||

`InsertEmission` | Symbol emission probabilities in the INSERT state. Either of the following: | ||

`NullEmission` | Symbol emission probabilities in the MATCH and INSERT states for the NULL model. Either of the following: A 1-by- `AlphaLength` row vector. Defaults to a uniform distribution.A structure containing residue counts, such as returned by `aacount` or`basecount` .
| ||

`BeginX` | BEGIN state transition probabilities. Format
is a 1-by- [B->D1 B->M1 B->M2 B->M3 .... B->Mend]
Default is | ||

`MatchX` | MATCH state transition probabilities. Format
is a 4-by- [M1->M2 M2->M3 ... M[end-1]->Mend; M1->I1 M2->I2 ... M[end-1]->I[end-1]; M1->D2 M2->D3 ... M[end-1]->Dend; M1->E M2->E ... M[end-1]->E ]
Default is | ||

`InsertX` | INSERT state transition probabilities. Format
is a 2-by- [ I1->M2 I2->M3 ... I[end-1]->Mend; I1->I1 I2->I2 ... I[end-1]->I[end-1] ]
Default is | ||

`DeleteX` | DELETE state transition probabilities. Format
is a 2-by- [ D1->M2 D2->M3 ... D[end-1]->Mend ; D1->D2 D2->D3 ... D[end-1]->Dend ]
Default is | ||

`FlankingInsertX` | Flanking insert states (N and C) used for LOCAL profile alignment. Format is a 2-by-2 matrix: [N->B C->T ; N->N C->C]
Default is | ||

`LoopX` | Loop states transition probabilities used for multiple hits alignment. Format is a 2-by-2 matrix: [E->C J->B ; E->J J->J]
Default is | ||

`NullX` | Null transition probabilities used to provide scores with log-odds values also for state transitions. Format is a 2-by-1 column vector: [G->F ; G->G]
Default is | ||

`IDNumber` | Optional. User-assigned identification number. | ||

`Description` | Optional. User-assigned description of the model. |

An HMM profile model is a common statistical tool for modeling structured sequences composed of symbols. These symbols include randomness in both the output (emission of symbols) and the state transitions of the process. Markov models are generally represented by state diagrams.

The following figure is a state diagram for an HMM profile of length four. INSERT, MATCH, and DELETE states are in the center section.

INSERT state represents the excess of one or more symbols in the target sequence that are not included in the profile.

MATCH state means that the target sequence is aligned to the profile at the specific location.

DELETE state represents a gap or symbol absence in the target sequence (also known as a silent state because it does not emit any symbols).

Flanking states (`S`

, `N`

, `B`

, `E`

, `C`

, `T`

)
are used for proper modeling of the ends of the sequence, either for
global, local or fragment alignment of the profile. `S`

, `B`

, `E`

,
and `T`

are silent, while `N`

and `C`

are
used to insert symbols at the flanks.

**Creating an HMM Profile Structure**

Create an HMM profile structure with 100 MATCH states, using the amino acid alphabet.

hmmProfile = hmmprofstruct(100,'Alphabet','AA') hmmProfile = ModelLength: 100 Alphabet: 'AA' MatchEmission: [100x20 double] InsertEmission: [100x20 double] NullEmission: [1x20 double] BeginX: [101x1 double] MatchX: [99x4 double] InsertX: [99x2 double] DeleteX: [99x2 double] FlankingInsertX: [2x2 double] LoopX: [2x2 double] NullX: [2x1 double]

**Editing an HMM Profile Structure**

Use the

`pfamhmmread`

function to create an HMM profile structure from`pf00002.ls`

, a PFAM HMM-formatted file included with the software.`hmm02 = pfamhmmread('pf00002.ls');`

Modify the HMM profile structure to force a global alignment by setting the looping transition probabilities in the flanking insert states to zero.

`hmm02 = hmmprofstruct(hmm02,'FlankingInsertX',[0 0;1 1]); hmm02.FlankingInsertX ans = 0 0 1 1`

`aacount`

| `basecount`

| `gethmmprof`

| `hmmprofalign`

| `hmmprofestimate`

| `hmmprofgenerate`

| `hmmprofmerge`

| `pfamhmmread`

| `showhmmprof`

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