pfamhmmread - Read data from PFAM HMM-formatted file

Either of the following:

• String specifying a file name, a path and file name, or a URL pointing to a file. The referenced file is a PFAM HMM-formatted file. If you specify only a file name, that file must be on the MATLAB search path or in the current folder.

• MATLAB character array that contains the text of a PFAM-HMM-formatted file.

Tip   You can use the gethmmprof function with the 'ToFile' property to retrieve HMM profile information from the PFAM database and create a PFAM HMM-formatted file.

Note   AlphaLength is 20 for 'AA' and 4 for 'NT'.

Symbol emission probabilities in the MATCH states.

The format is a matrix of size ModelLength-by-AlphaLength, where each row corresponds to the emission distribution for a specific MATCH state.

Symbol emission probabilities in the INSERT state.

The format is a matrix of size ModelLength-by-AlphaLength, where each row corresponds to the emission distribution for a specific INSERT state.

Symbol emission probabilities in the MATCH and INSERT states for the NULL model.

The format is a 1-by-AlphaLength row vector.

Note   NULL probabilities are also known as the background probabilities.

BEGIN state transition probabilities.

Format is a 1-by-(ModelLength + 1) row vector:

[B->D1 B->M1 B->M2 B->M3 .... B->Mend]

MATCH state transition probabilities.

Format is a 4-by-(ModelLength - 1) matrix:

[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  ]

INSERT state transition probabilities.

Format is a 2-by-(ModelLength - 1) matrix:

[ I1->M2 I2->M3 ... I[end-1]->Mend;
  I1->I1 I2->I2 ... I[end-1]->I[end-1] ]

DELETE state transition probabilities.

Format is a 2-by-(ModelLength - 1) matrix:

[ D1->M2 D2->M3 ... D[end-1]->Mend ;
  D1->D2 D2->D3 ... D[end-1]->Dend ]

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]

Loop states transition probabilities used for multiple hits alignment.

Format is a 2-by-2 matrix:

[E->C  J->B ;
 E->J  J->J]

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]