I have a set of nucleotide sequences for which I have aligned using Clustal Omega. In particular, I performed a full alignment, and obtained a full distance matrix.
The distance matrix scores range between 0 and 1. I am looking to use this score to back-compute the number of different positions present in the alignment. Is this possible? If possible, I'm looking to avoid using code (my own or otherwise) to re-compute the number of positions differing between each pair of segments, and instead compute it directly from the distance score.
•
written
by
ericmajinglong
1 answer
I believe Clustalo provides uncorrected pairwise distances, so you can multiply your distance by the length of the sequence to obtain the number of differences between two sequences.
Log in to answer this question.
-
What exactly is Biopython's alignment.score variable?
written by Tom •
-
Percent identity matrix from ClustalOmega/Clustalw with Biopython
written by sean.cascarina •
-
Clustal Omega alignment algorithm - does it account for codons and open reading frames (ORF)?
written by manaswwm
-
Interpreting distance from clustal omega
written by Natasha •
-
alignment score and other values for the whole paired-end alignment (with overlap)
written by shim •
-
Aligning Copies Of A Protein Domain To A Pfam Model (HMM)
written by UnivStudent
-
How to compute a node similarity matrix for two graphs?
written by ishanee.india •
-
Multiple Sequence Alignment - Appending To An Alignment
written by ericmajinglong
-
Compute Affinity Matrix From Distance Matrix
written by ericmajinglong
-
Pairwise Sequence Alignment Of A Collection Of Proteins Scores In Matrix Format
written by Azam •
