Question: Strange characters ^? in fasta format sequence file
0
gravatar for 860101959
3 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

sequence • 216 views
ADD COMMENTlink modified 3 months ago • written 3 months ago by 86010195910
3
gravatar for Pierre Lindenbaum
3 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum122k wrote:

what is the output of

file your.fasta

must be : ASCII test

ADD COMMENTlink written 3 months ago by Pierre Lindenbaum122k

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 3 months ago by lieven.sterck5.5k

Thanks, I think it is encoding problem.

ADD REPLYlink written 10 weeks 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 10 weeks ago by Pierre Lindenbaum122k
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