gravatar for Dineshkumar K

2 hours ago by

Kasaragod, Kerala, India

I need to concatenate clustalw aligned multifasta alignment file. I have tried many concatenating tools, which is not recognising the gaps (---) of the alignment and ultimately end up with error stating that sequence dissimilar length. Is there any way to do the same.
For example
I have alignment file a.fasta and b.fasta as given below,

a.fasta
>or1
ATGTCT-----TGA
>or2
-----TGATAG-----
>or3
TGATA-----TAGTT

b.fasta
>or2
ATGATGTATGATGATA
>or1
GTAGATAGATAGAG
>or3
ATGCTAGATAGATAG

The expected output is given below,

c.fasta
>or1
ATGTCT-----TGAGTAGATAGATAGAG
>or2
-----TGATAG-----ATGATGTATGATGATA
>or3
TGATA-----TAGTT ATGCTAGATAGATAG



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