Entering edit mode
5.7 years ago
Chris
▴
30
I have two very long sequences (about 200Kb) each that I have aligned using Kalign from EBI. I include a preview . I was wondering if there is any way to calculate transitions (A to G and C to T and vice versa) and transversions (A to C, A to T, G to C and C to T and vice versa) on those aligned sequences. Any help will be highly appreciated.
Thank you for your time
CLUSTAL multiple sequence alignment by Kalign (2.0)
Pio GAGGAGCACGAGCTGTGAGCTACGAACCGCCGGTCCGCGTCGAGATCCCGAGCGAGCTGC
Bxz1 GAGGAGCACGAGCTGTGAGCTACGAACCGCCGGTCCGCGTCGAGATCCCGAGCGAGCTGC
Pio TGCCCCTGATACACCTGGTGGCCGAGCATCATGGCGTCTCGCCTCAGACCGTCGCTGTCG
Bxz1 TGCCCCTGATACACCTGGTGGCCGAGCATCATGGCGTCTCGCCTCAGACCGTCGCTGTCG
Pio CCTGGATGACCTACGGCGCCGAGAACTCCTGCACCGAGGACGACATCAGGGACATGGTTG
Bxz1 CCTGGATGACCTACGGCGCCGAGAACTCCTGCACCGAGGACGACATCAGGGACATGGTTG
Pio CCAAGCGGGGTGAGCGCATCCATGCCGGATTCCAGCGCTTCCTCAAAGATCACCTCGTCG
Bxz1 CCAAGCGGGGTGAGCGCATCCATGCCGGATTCCAGCGCTTCCTCAAAGATCACCTCGTCG
Pio GCAATCGCAAGAACCGGCTCGGCGGACGATGACCATGCCCTGTCAGCAGAGGGTCCAGAC
Bxz1 GCAATCGCAAGAACCGGCTCGGCGGACGATGACCATGCCCTGTCAGCAGAGGGTCCAGAC
Pio CGCCTTCGCCATCGCTGTGTTGGCCCTCGTCATCGGCCTGATCGGGTGGGTGCACGAGAC
Bxz1 CGCCTTCGCCATCGCTGTGTTGGCCCTCGTCATCGGCCTGATCGGGTGGGTGCACGAGAC
Pio GTGCCTACAGGACGAGACAAATCAGAATCCTGGCGTGCAGCACACCGACTACAATTGTCC
Bxz1 GCGCCTACAGGACGAGACAAATCAGAATCCTGGCGTGCAGCACACCGACTACAATTGTCC
Pio TGTTGCCACACTGTCACACCCCTACACCCACACTGCAGGAGGACTATAGGCTATGAGTGT
Bxz1 TGTTGCCACACTGTCACACCCCTACACCCACACTGCAGGAAGACTATAGGCTATGAGTGT
Interested if others are aware of more direct methods, but have you looked at this post, which uses BioPython to process an alignment?
Using the same approach, if you can output your Kalign 2.0 alignment in any format supported by BioAlignIO, you could write a short script to iterate through each column in the alignment, and enumerate the transitions and transversions.
Thanks for the tip but the link does not work
Link edited.