Question: Exonerate ** FATAL ERROR **: Unrecognised symbol 'J' (ascii:74)
0
gravatar for jomaco
4.5 years ago by
jomaco190
European Union
jomaco190 wrote:

Hi,

 

I am receiving the following error when running exonerate-2.2.0:

** FATAL ERROR **: Unrecognised symbol 'J' (ascii:74)

 

Here are a couple of examples of where this occurs:

 

** FATAL ERROR **: Unrecognised symbol 'J' (ascii:74) file:[../../blastdb/evidence_aln_seqs/output2/evidence.seqmasked.cat.1-nopipe.split.4.fa] seq:[gi614497259gbAHX42233.1] pos:[267]

>gi614497259gbAHX42233.1
FNIFIRGLFENMKVEEAISVWQVLQEDGCVADSTTYGVLIHGFCKNGYLNKALWVLTDAE
DKGNDLDVFAYSSIINGLCNARRVDEGFDTLDRMTKHGCKPNAHVCNTLLNGLIRASKID
DAIRFFSEMAAKDCLXTVVTYNTLIDGLCKVERFDEAYLLVKEMLEKGWKPDIITYSLLM
RGLCQDKKIDMALNLWCQVVEKGLKPDVIMHNIIIHGLCSAGKVGDALQLYLRMSQCDCV
PNLVTLNTLMEGFYRARDCLNASVIWARJLRSGLKPDJISYNIVLKGLCSCIDY

 

** FATAL ERROR **: Unrecognised symbol 'J' (ascii:74) file:[../../blastdb/evidence_aln_seqs/output2/evidence.seqmasked.cat.1-nopipe.split.3.fa] seq:[gi614497313gbAHX42260.1] pos:[302]

>gi614497313gbAHX42260.1
IKGGFEIWELMGRDGVRNIFSFNILIRGLFESRKVEEAISVWQVLQENGCAADSTTYGVL
IHGFCKNGYLNKALLVLTEAENKRNDLDVFAYSSIINGLCNARRVDEAFDMIDRMAKHGC
KPNAHVCNTLLNGLIRASKIEDAIRFFTDMASKNCLPTVVTYNTLINGLCKAERFDVAYL
LVKEMLEKEWKPDIITYSLLMRGLCQGKKIDMALNLWCQVVEKGLKPDVIMHNIIIHGLC
SAGKVEDALQLYLKMSQCDCVPNLVTLNTLMDGFYKARDCLNASVIWARILRSGLKPDII
SYNJVLKGLCSCYRIS

 

Has anyone else had this problem? I don't understand why 'J' is an unrecognised character.

Hope you can help.

 

ADD COMMENTlink modified 4.5 years ago by Pawel Szczesny3.2k • written 4.5 years ago by jomaco190
3
gravatar for Pawel Szczesny
4.5 years ago by
Pawel Szczesny3.2k
Poland
Pawel Szczesny3.2k wrote:

J is a placeholder "used in cases where chemical or crystallographic analysis of a peptide or protein cannot conclusively determine the identity of a residue." It does not represent a proteinogenic amino acid (but an amibiguity between I and L) and exonerate does not have a translation table for it. Replace it either with leucine or isoleucine.

ADD COMMENTlink written 4.5 years ago by Pawel Szczesny3.2k

Thanks, very informative. Perhaps it would be best to remove these sequences, rather than guess (I'm not sure which I would choose)? They form part of a large evidence set so are not necessarily required.

ADD REPLYlink written 4.5 years ago by jomaco190

I would not remove it, unless you require from exonerate 100% agreement (this is not recommended BTW) or mismatch codon can ruin your analysis.

ADD REPLYlink written 4.5 years ago by Pawel Szczesny3.2k

Sorry, to clarify, I mean to remove the whole sequence (i.e. any sequence containing "J") in my dataset. These sequences are part of a set of over 500,000 protein sequences from asterids species related to my species of interest, to be used as evidence alignments, so it should not affect the analysis too much. This should be OK? (as apposed to removing just the character itself). Thanks again

ADD REPLYlink written 4.5 years ago by jomaco190
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