Predict Prion like Proteins (PLAAC)

Question

[cvu]

Hi All,

I'm using PLAAC (http://plaac.wi.mit.edu/) to identify probable prion subsequences in my protein sequences. but I get different LLR scores for same protein sequence, when I give fasta and multifasta files.

Output from FASTA file

SEQid   MW      MWstart MWend   MWlen   LLR     LLRstart        LLRend  LLRlen  NLLR    VITmaxrun       COREscore    COREstart        COREend CORElen PRDscore        PRDstart        PRDend  PRDlen  PROTlen HMMall  HMMvit  COREaa  STARTaa       ENDaa   PRDaa   FInumaa FImeanhydro     FImeancharge    FImeancombo     FImaxrun        PAPAcombo       PAPAprop      PAPAfi  PAPAllr PAPAllr2        PAPAcen PAPAaa
lcl|JN627160.1_prot_AEV89713.1_276 [gene=OBP_276] [protein=putative structural lysozyme] [protein_id=AEV89713.1] [location=complement(250739..258037)]        14      161     240     80      -5.348  705     764     60      -0.089  0    NaN      0       -1      0       0.000   0       -1      0       2432    -2.070  -2.481  -       -       -       -    903      0.449   0.002   0.096   87      -0.053  -0.053  -0.002  -0.304  -0.285  703     IDLLRSTGNEQMLRDLGVIYTENGMDRINMQIFHDRFAQYM

Output from Multifasta file

SEQid   MW  MWstart MWend   MWlen   LLR LLRstart    LLRend  LLRlen  NLLR    VITmaxrun   COREscore   COREstart   COREend CORElen PRDscore    PRDstart    PRDend  PRDlen  PROTlen HMMall  HMMvit  COREaa  STARTaa ENDaa   PRDaa   FInumaa FImeanhydro FImeancharge    FImeancombo FImaxrun    PAPAcombo   PAPAprop    PAPAfi  PAPAllr PAPAllr2    PAPAcen PAPAaa
lcl|JN627160.1_prot_AEV89713.1_276 [gene=OBP_276] [protein=putative structural lysozyme] [protein_id=AEV89713.1] [location=complement(250739..258037)]  14  161 240 80  3.351   1972    2031    60  0.056   0   NaN 0   -1  0   0.000   0   -1  0   2432    -1.468  -2.481  -   -   -   -   903 0.449   0.002   0.096   87  -0.053  -0.053  -0.002  -0.341  -0.300  703 IDLLRSTGNEQMLRDLGVIYTENGMDRINMQIFHDRFAQYM

From Fasta I got LLR score -5.348, while from multifasta I got 3.351 for the same protein.

I don't understand why the score is changes. Please help Any help would be appreciated Thanks

[microfuge]

It may be due to setting of Alpha which when set to 100 calculate the background frequencies from the input sequences. Two suggestions as given here (http://plaac.wi.mit.edu/details) would be to a) Input complete proteome fasta or b) Set alpha by choosing the background frequency to particular organism from the dropdown list which appears when the alpha slider is moved from 100.

[cvu]

Thanks for the reply microfuge