Question: How to change sequence format in my alignment file?
1
gravatar for Adam
5 weeks ago by
Adam40
Adam40 wrote:

Hello,

I have fasta file with alingned several sequences (from MUSCLE), when I open it (e.g. notepad++) they look like: this

And I want dot format of identities like

this

and then save it in txt file.

I failed using MEGA, BioEdit and CodonCode, how can I do this?

alignment sequence • 180 views
ADD COMMENTlink modified 2 days ago by Biostar ♦♦ 20 • written 5 weeks ago by Adam40
1

Have you tried Jalview (LINK)?

ADD REPLYlink written 5 weeks ago by genomax85k

Yes, I installed it and it does't even start...

ADD REPLYlink written 5 weeks ago by Adam40

If you are not able to install try one of the older versions that used webstart.

ADD REPLYlink written 5 weeks ago by genomax85k

Thanks, i got it. But I'm still undable to save it (dots instead of nucleotides)

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by Adam40

Please use these directions: How to add images to a Biostars post

ADD REPLYlink written 5 weeks ago by genomax85k

I failed using MEGA, BioEdit and CodonCode

What issues were you running into? Did the tools not run at all or did the results not look like what you had hoped for?

ADD REPLYlink written 5 weeks ago by Friederike5.7k

MEGA crashed during export (xls, xlsx). Csv went fine but only 1kb have been exported. I have alignment of 40 sequences, ~25kb each. BioEdit - I was abe to change letters to dots, but each export always contained letters. CodonCode - here I exported what I want but only positions with changes.

ADD REPLYlink written 5 weeks ago by Adam40

CodonCode - here I exported what I want but only positions with changes.

Isn't that what you wanted?

ADD REPLYlink written 5 weeks ago by Friederike5.7k

I was looking for full sequences but I'll be content with this result

ADD REPLYlink written 5 weeks ago by Adam40
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