I'm learning about CRISPR at my college. I understand that when viral DNA is inserted into a bacterial cell, the **Cas1-Cas2** proteins identify the **PAM** …
How can I calculate a Levenshtein distance (edit distance) in R (for DNA) with a custom substitution matrix that scores transversions and transitions differently? No, …
Trying to understand substitution matrices. It seems like it is a scoring scheme for alignments, particularly if you are looking for homology? I am trying …
I have what is probably a very basic question about how substitution models play in to obtaining distance measures between protein sequences. To briefly summarize …
<p>I'm looking for a substitution matrix for aligning short DNA sequences using <a href='http://www.chick.manchester.ac.uk/SiteSeer/IUPAC_codes.html'>IUPAC nucleotide ambiguity codes</a>. I would guess there are existing solutions but …
<p>Every PAM substitution matrix on the web begins with a line like</p> <pre><code># This matrix was produced by "pam" Version 1.0.6 [28-Jul-93] </code></pre> <p>or version …