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What does PolyPhen-2 error mean?

Hi all,

I'm trying use PolyPhen-2 to analyse my protein data. The input is a protein sequence, but I got the error:

ERROR: _calc_ident() Lengths of sequences do not match (len1=565, len2=507)
 at /net/projects/ggi/pph2/perl/PPH/Align.pm line 1618
    PPH::Align::_calc_ident('MAMAEQEVYKYLYKDDIHPVQLLNAFKSFNDHGLFTDVTLCASGVNFQCHKAVLAACSNYF...', 'AG------GLSDGNGINGLIEWKRHMEGVKAELVEEMSCHLKDLLDKAVAETMHSYKRSAL...') called at /net/projects/ggi/pph2/perl/PPH/Align.pm line 1077
    PPH::Align::ident_fij_scores('HASH(0x70ddd40)', 'SNP=HASH(0x7155290)') called at /net/projects/ggi/pph2/perl/PPH/Profile.pm line 278
    PPH::Profile::set_PSIC_profile('HASH(0x70ddd40)', 'SNP=HASH(0x7155290)') called at /net/projects/ggi/pph2/perl/PPH.pm line 490
    PPH::analyze('PPH=HASH(0x7140e10)', 'SNP=HASH(0x7155290)') called at /net/projects/ggi/pph2/bin/run_pph.pl line 359

Why I got this error? I blast my sequence in NCBI, use uniprot database, The first match is a protein from mouse, query cover is 99%, identity is 77%, mouse sequence length is 558, I also used uniprot blast, the first match is a reptile protein, length is 558. Why the error said len2=507? How can I know which protein sequence does polyphen-2 used? How can I fix this error? Thank you!

polyphen-2
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updated by Ram Ram • written by Jl • Jl

1 answer

Used shorter tittle for sequence and solved it.

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written by Jl • Jl

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