TMHMM: difference between online and local handling of sequences with a U

[richelbilderbeek]

Sent the following email to prof Kroch on 2021-01-15 9:35:

Dear professor Krogh,

With this email I ask for your insights in why TMHMM responds differently online compare to local usage, regarding the dis/allowance of a U in the protein sequence.

I have a FASTA file with a U in both of the two sequences (FASTA file is also attached):

with_u_fasta.zip

>sp|Q9NZV6|MSRB1_HUMAN Methionine-R-sulfoxide reductase B1 OS=Homo sapiens (Human) OX=9606 GN=MSRB1 PE=1 SV=3
MSFCSFFGGEVFQNHFEPGVYVCAKCGYELFSSRSKYAHSSPWPAFTETIHADSVAKRPE
HNRSEALKVSCGKCGNGLGHEFLNDGPKPGQSRFUIFSSSLKFVPKGKETSASQGH
>sp|Q9Y6D0|SELK_HUMAN Selenoprotein K OS=Homo sapiens (Human) OX=9606 GN=SELENOK PE=1 SV=3
MVYISNGQVLDSRSQSPWRLSLITDFFWGIAEFVVLFFKTLLQQDVKKRRSYGNSSDSRY
DDGRGPPGNPPRRMGRINHLRGPSPPPMAGGUGR

Running it locally gives a clear error:

richel@N141CU:~/.local/share/tmhmm-2.0c$ ./bin/decodeanhmm.Linux_x86_64 lib/TMHMM2.0.model ~/with_u.fasta -f lib/TMHMM2.0.options
decodeanhmm 1.1g
Copyright (C) 1998 by Anders Krogh
Fri Jan 15 09:26:44 2021

Model in file "lib/TMHMM2.0.model" parsed successfully.
Character 'U' not allowed in alphabet 'ACDEFGHIKLMNPQRSTVWYBXZ'.
Error in sequence sp|Q9NZV6|MSRB1_HUMAN Methionine-R-sulfoxide reductase B1 OS=Homo sapiens (Human) OX=9606 GN=MSRB1 PE=1 SV=3
label=0 HNRSEALKVSCGKCGNGLGHEFLNDGPKPGQSRFUIFSSSLKFVPKGKETSASQGH

Running it online works without error (see the attached screenshot). I do notice at the bottom of the attached screenshot, that there is a warning. AFAICS, there is no way to see the warning's message.

What is the difference between online version of TMHMM compared to its local usage, regarding the dis/allowance of a U in the protein sequence?

Thanks for your help, Richel Bilderbeek

[richelbilderbeek]

Correct email of Krogh is at http://people.binf.ku.dk/krogh/ , I also informed the webmaster :+1: