Hello,
I have been using the OMA database to retrieve orthologs between human and other species. I am specifically using the function getProtein("proteinID", attribute = "orthologs") from the OmaDB R package. Example: getProtein("P01112", attribute = "orthologs").
This function outputs a table with many columns, one of them named distance, which I believe contains the evolutionary distance between the orthologs. Does anyone know which algorithm and what sort of information is integrated together into this final distance score?
Best wishes, Abel
•
written
by
Abel Sousa •
1 answer
Dear Abel,
this is the ML distance estimate for the optimal pairwise local alignment (Smith-Waterman) using the Gonnet scoring matrices.
Best wishes
Adrian
Log in to answer this question.
-
Optimizing DNA Sequence Subset Selection for Balanced Base Distribution: Seeking Solutions for Smal…
written by samuelknudsen •
-
Job: Postdoctoral Research position in Bioinformatics and Comparative Genomics
written by sina.majidian •
-
Job: Group Leader - Theory@EMBL and Developmental Biology Unit
written by EMBL Recruitment •
-
Transcritomes comparison - How can you get a weighted mapping given two species?
written by Yotam ConstantiniBiostar •
-
Tutorial: Unsupervised clustering on gene expression data
written by Hamid Ghaedi
-
Differentially Expressed Unigenes (DEGs)
written by wes •
-
Clustering with Sleipnir
written by crouch.k •
-
Sequencing Strandedness and Differences in Expression Readouts Between stringtie and htseq
written by kmhum •
-
News: Eukaryotic metabarcoding (EUKB01)
written by oliverhooker
-
News: WORK SHOP Eukaryotic metabarcoding
written by oliverhooker
I don't know the exact answer to your question. Odds are that distance is some kind of a function that is inversely proportional to sequence identity.