Question: Strange characters ^? in fasta format sequence file
0
gravatar for 860101959
14 months ago by
86010195910
86010195910 wrote:

Recently, I received a fasta format sequence file from one of my colleges, But there are some strange characters like ^? in the sequence , does anyone knows why and how can I delete these characters? Because there are a lot of ^? in sequences and I don't want to delete manually.

I tried to recognize these characters using vim by \^\? , ^? or \^? but failed. Since the data is output of MEGA maybe there is some reasons in there.

The sequence is like this: ^?MRATGEKRVLQLHELDEFCLDSYENAKIYKEKTERWHNRHIREKEIEVGQQVLMFNSHLKLFSGKLKSRWSGSFTVVAVFPHSKLERIAEDLLIE

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ADD COMMENTlink modified 14 months ago • written 14 months ago by 86010195910
3
gravatar for Pierre Lindenbaum
14 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum129k wrote:

what is the output of

file your.fasta

must be : ASCII test

ADD COMMENTlink written 14 months ago by Pierre Lindenbaum129k

apart from Pierre Lindenbaum remark, does the file contain the typical fasta header lines (starting with > followed by some text denoting the sequence ID/name) ?

ADD REPLYlink written 14 months ago by lieven.sterck8.0k

Thanks, I think it is encoding problem.

ADD REPLYlink written 13 months ago by 86010195910

If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.

Upvote|Bookmark|Accept

ADD REPLYlink written 13 months ago by Pierre Lindenbaum129k
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