Calculate pair-wise dissimilarity of DNA sequences in Python

Is there any available package in Python that can calculate dissimilarity between two DNA sequences using any alignment algorithm?

Thanks!

python dna sequence similarity alignment

• 3,452 views • link

updated 4.1 years ago by Ram

• written 11.3 years ago by songzewei •

1 answer

Maybe find the similarity and use the complement?

• 0 views • link

written 11.3 years ago by Ram

yes, but I would like to know if there is any library or script available out there.

• 0 views • link

written 11.3 years ago by songzewei •

I guess you could use EMBOSS needle or water wrapped in BioPython: http://biopython.org/DIST/docs/_api_159/Bio.Emboss.Applications-module.html

• 0 views • link

written 11.3 years ago by Ram

More posts like this

What exactly is Biopython's alignment.score variable?
written 2.0 years ago by Tom •

Hello, I can see from reading onto that Biopython's Align.PairwiseAligner.align.score() variable is: 'Calling the "score" method on the aligner with two sequences as arguments will …
overlapping nucleotides in sequence alignment
written 10.4 years ago by zhaochaoyang2009 •

Hi, Is there a way to calculate the overlapping nucleotides numbers between every two DNA sequences by doing multiple sequence alignment? I would like to …
r for RNA/RNA hybrid free energy
written 10.8 years ago by I0110

Hi everyone, I was trying to calculate the hybrid free energy between two RNA sequences. Is there any R function that can carry out this …
Trimming an alignment in R
written 10.9 years ago by Gon •

Hi! I was wondering if anyone could help. I'm using the package ape in R and I want to trim an alignment of class DNAbin, …
Different calculation of Bray-Curtis dissimilarity in vegan (R) and mothur?
written 11.3 years ago by songzewei •

The Bray-Curtis dissimilarity using vegdist of the vegan package in R is calculated as the sum of absolute difference between each pair of OTU: `bray` …
How to calculate percentage identity/error rate from local alignment score?
written 12.3 years ago by crivenster

Hi, I have a local alignment on similar sequences using Smith-Waterman algorithm. I have alignment scores generated,how to calculate the percentage identity between the sequences? …
Pdb Structures Go Terms Clustering And Distance
written 14.5 years ago by Reyhaneh

Hi; I have two questions regarding Go terms; 1) I would clusters of PDB proteins using their Go Terms. Are there any available datasets for …
Finding Protein Sequence Coverage With R Or Python
written 14.6 years ago by Lakshmi •

Hello, I am trying to find protein sequence coverage after pairwise sequence alignment by using the following formula sequence coverage = (length of aligned residues/length …
Which Method Is The Best Dissimilarity Measurement For Hierarchical Clustering Of Dna Methylation D…
written 14.7 years ago by Gangcai

Dear all, I have performed hierarchical clustering for bisulfite DNA methylation data using two different dissimilarity methods: euclidean distance and pearson correlation by using R …
Is There Any Script To Count Repeats In Protein Sequences?
written 15.3 years ago by Mohammad Reza Bakhtiarizadeh

Hi, there are several script to count simple sequence repeat (SSR) in dna sequences (like MISA). i want to know that is there any script …