Question: Error characters in fasta file
0
gravatar for atitparajuli2018
8 weeks ago by
atitparajuli20180 wrote:

How do I remove invalid characters E, F, I, L, P, Q from a fasta file?

I get these invalid characters while running muscle command for multiple sequence alignment.

muscle alignment fasta • 233 views
ADD COMMENTlink modified 8 weeks ago by zx87548.0k • written 8 weeks ago by atitparajuli20180
1

It's amino acid code. Does it assume the input is DNA for some reason?

ADD REPLYlink written 8 weeks ago by Asaf6.1k

Yes it does. Can I clean these characters from the file?

ADD REPLYlink written 8 weeks ago by atitparajuli20180
1

No, you should make sure your input is DNA

ADD REPLYlink written 8 weeks ago by Asaf6.1k

Please can you help me with the muscle command line for that?

ADD REPLYlink written 8 weeks ago by atitparajuli20180
1

Please read the manual, especially section 3. Asking us to do your work for you is not good etiquette.

ADD REPLYlink written 8 weeks ago by RamRS23k

I did use the -seqtype nucleo option in the muscle command still I was getting the error message so I was asking for the code that does not give an error message as: I* ERROR * Invalid parameter -SeqType nucleo

ADD REPLYlink written 8 weeks ago by atitparajuli20180
2

That doesn't change the fact that your sequences aren't nucleotides.

ADD REPLYlink written 8 weeks ago by jrj.healey13k

You already have an answer - you can only align multiple sequences of a single type (protein/DNA) using muscle. If you're sure your sequences are of the same type, we can help you with any error message you're seeing.

ADD REPLYlink written 8 weeks ago by RamRS23k
1

Dear, In a nucleotide fasta file, you won't be able to get this type of error. Make sure you have DNA file. And for muscle command please try this simple one and check you are getting the desired result

muscle -in seqs.fa -out seqs.afa
ADD REPLYlink written 8 weeks ago by archana.bioinfo87160

Asaf has already stated the point you're trying to make - what is the value you're adding to the discussion?

ADD REPLYlink written 8 weeks ago by RamRS23k
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