Read data from PFAM HMMformatted file
HMMStruct
= pfamhmmread(File
)
File  Either of the following:

HMMStruct  MATLAB structure containing information from a PFAM HMMformatted file. 
Note:

reads HMMStruct
= pfamhmmread(File
)File
,
a PFAM HMMformatted file, and converts it to HMMStruct
,
a MATLAB structure containing the following fields corresponding
to parameters of an HMM profile:
Field  Description  

Name  The protein family name (unique identifier) of the HMM profile record in the PFAM database.  
PfamAccessionNumber  The protein family accession number of the HMM profile record in the PFAM database.  
ModelDescription  Description of the HMM profile.  
ModelLength  The length of the profile (number of MATCH states).  
Alphabet  The alphabet used in the model, 'AA' or 'NT' .
 
MatchEmission  Symbol emission probabilities in the MATCH states. The
format is a matrix of size  
InsertEmission  Symbol emission probabilities in the INSERT state. The
format is a matrix of size  
NullEmission  Symbol emission probabilities in the MATCH and INSERT states for the NULL model. The format is a 1by
 
BeginX  BEGIN state transition probabilities. Format
is a 1by [B>D1 B>M1 B>M2 B>M3 .... B>Mend]  
MatchX  MATCH state transition probabilities. Format
is a 4by [M1>M2 M2>M3 ... M[end1]>Mend; M1>I1 M2>I2 ... M[end1]>I[end1]; M1>D2 M2>D3 ... M[end1]>Dend; M1>E M2>E ... M[end1]>E ]  
InsertX  INSERT state transition probabilities. Format
is a 2by [ I1>M2 I2>M3 ... I[end1]>Mend; I1>I1 I2>I2 ... I[end1]>I[end1] ]  
DeleteX  DELETE state transition probabilities. Format
is a 2by [ D1>M2 D2>M3 ... D[end1]>Mend ; D1>D2 D2>D3 ... D[end1]>Dend ]  
FlankingInsertX  Flanking insert states (N and C) used for LOCAL profile alignment. Format is a 2by2 matrix: [N>B C>T ; N>N C>C]  
LoopX  Loop states transition probabilities used for multiple hits alignment. Format is a 2by2 matrix: [E>C J>B ; E>J J>J]  
NullX  Null transition probabilities used to provide scores with logodds values also for state transitions. Format is a 2by1 column vector: [G>F ; G>G] 
For more information on HMM profile models, see HMM Profile Model.
Read a locally saved PFAM HMMformatted file into a MATLAB structure.
pfamhmmread('pf00002.ls') ans = Name: '7tm_2' PfamAccessionNumber: 'PF00002.15' ModelDescription: '7 transmembrane receptor (Secretin family)' ModelLength: 293 Alphabet: 'AA' MatchEmission: [293x20 double] InsertEmission: [293x20 double] NullEmission: [1x20 double] BeginX: [294x1 double] MatchX: [292x4 double] InsertX: [292x2 double] DeleteX: [292x2 double] FlankingInsertX: [2x2 double] LoopX: [2x2 double] NullX: [2x1 double]
gethmmalignment
 gethmmprof
 hmmprofalign
 hmmprofstruct
 showhmmprof