There is a very good reason as to why the VCF Splitter is CATE's most important function. CATE requires a very specific file structure to function. To create this file structure we use the VCF splitter tool. But first, let us learn a bit about what this file structure is. CATE function...
*/ private void identifyResidue(int pos) { HashMap<String, ArrayList<String>> codons = assembleCodonMap(); // Set base position of first codon in the CDS (to be retrieved from GenBank later) int posOfCDS = 276; // Adjust given codon count to account for any difference between CDS /...
The probability of finding an antisense stop codon in frame 1, is equivalent to the probability of finding the 128 allowed dicodons. In contrast, antisense stop codons in frame 2 can overlap with all the possible 192 dicodons, and their probabilities are thus unaffected by the overlap (see ...
We ignore second-order terms where we incorrectly read one mutation as another, as such errors will be very rare as mutations themselves are rare (most codons are wildtype in most sequences). We next adjust all of the deep sequencing codon counts in the antibody-selected and mock-selected ...
Influenza virus can escape most antibodies with single mutations. However, rare antibodies broadly neutralize many viral strains. It is unclear how easily influenza virus might escape such antibodies if there was strong pressure to do so. Here, we map al