Predict Prion like Proteins (PLAAC)
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
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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.
Thanks for the reply microfuge