How to calculate base pair conservation for two species?
Hi,
I'm trying to represent pair-wise conservation in the mitochondrial genome across a number of species. I want to create a diagram that looks like this. In the lower-right corner, there is a note that explains how conservation has been illustrated. I'd like to calculate average conservation for the genome and a given window.
I'd like to know how to get a conservation score for every base, given the sequences of two species. Is there an alternative for PhyloP or PhastCons which seem to require MSA?
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Including reference genome in SNP-based phylogeny
written by maxrwjones •
-
Problem with obitools (obiconvert a simple fasta to ecopcr)
written by Daniel •
-
How to get nuclear and mitochondrial gene sequences ?
written by kA •
-
Looking for a database containing the least-conserved, most highly polymorphic SNPs (or regions) of…
written by fwuffy
-
What tools to compare 3 sets of predicted protein (gene) sequences
written by ngs_new_user •
-
Is there a way to fetch genomic sequences at given coordinates without downloading fasta files?
written by ericbrenner •
-
Identifying which allele is derived in non-human species
written by Rubal
-
Phylop Results Interpretation
written by Fedor Gusev
-
Number Of Reads Over A Given Window And Over Given Regions Bam Files
written by dfernan
-
Visualize Gene Descriptions On The Maps Of Ensembl Genome Browser
written by Anima Mundi
