This is a test version of Biostars. For the public version, visit https://www.biostars.org.
align two long sequences using Muscle but found gaps only

Hi all:

I got two long DNA sequences (> 40k bps) from two close species, but Muscle could not produce a correct alignment of them with no error message also.

the result is an alignment made by GAPs only.

Could you please help me to find the reason ?

Thanks in advance!

alignment
• 2,111 views • link
written by Pei Pei

Basically, you are using the wrong tool for the task you want. Try Mauve, BWA (not sure if it handles 40K long sequences, though) or even Blast.

edit: also, see this thread.

• 0 views • link
written by h.mon h.mon

Thanks for the reply!

• 0 views • link
written by Pei Pei

Try to use mafft. http://mafft.cbrc.jp/alignment/software/

mafft --thread 2 --localpair --maxiterate 1000 --ep 0.123 --legacygappenalty seq4.fa > seq4.aln

version 7

Or:

mafft --genafpair --maxiterate 1000 input_file > output_file

It may help. Good luck!

• 0 views • link
written by natasha.sernova natasha.sernova

0 answers

No answers yet.

Log in to answer this question.

More posts like this