1
$\begingroup$

I am trying to align the following 8 sequences using clustalo on ubuntu terminal using the following command. But I am not getting the right output.

clustalo -i sequence.fasta -o output.clu

My input file issequence.fasta with 8 sequences I downloaded from BLAST

My output file output.clu

enter image description here

The output I was hoping for outputOnline.clustal

Also I would appreciate if some can tell me how to share this kind of data in a question because obviously the way I have done is doesnot seem appropriate.

$\endgroup$
2
$\begingroup$

You just need to specify the output format with the outfmt flag.

clustalo -i sequence.fasta -o output.clu -outfmt=clu

should give you the desired output.


How to share data?

Try using an abbreviated example which people can copy&paste, for longer data you could use something like http://pastebin.com/ but the URL might expire.

gi|1709777|sp|P51780.1|PRIO_TRIVU MGKIQLGYWILVLFIVTWSDLGLCKKPKPRPGGGWNSGGSNRYPGQPGSPGGNRYPGWGHPQGGGTNWGQPHPGGSNWGQPHPGGSSWGQPHGGSNWGQGGYNKWKPDKPKT

gi|1709773|sp|P52114.1|PRIO_MUSPF MVKSHIGSWLLVLFVATWSDIGFCKKRPKPGGGWNTGGSRYPGQGSPGGNRYPPQGGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQPHGGGGWGQGGGSHGQWGKPSKPKT

gi|1709774|sp|P49927.1|PRIO_PIG MVKSHIGGWILVLFVAAWSDIGLCKKRPKPGGGWNTGGSRYPGQGSPGGNRYPPQGGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQPHGGGGWGQGGGSHGQWNKPSKPKT

$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.