Author: Bahir, Iris; Fromer, Menachem; Prat, Yosef; Linial, Michal
Title: Viral adaptation to host: a proteome-based analysis of codon usage and amino acid preferences Document date: 2009_10_13
ID: 629kl04a_19
Snippet: For a particular group of viruses and a given set of hosts, frequency vectors (20 element vectors for amino acids, and 59 element vectors for codons) were calculated. To compare these vectors, we measure the pairwise distance between codon usage (or amino acid distribution) using a distance metric, where lower values indicate greater similarity. We applied multiple measures to determine the distance between any pair of vectors for virus and host......
Document: For a particular group of viruses and a given set of hosts, frequency vectors (20 element vectors for amino acids, and 59 element vectors for codons) were calculated. To compare these vectors, we measure the pairwise distance between codon usage (or amino acid distribution) using a distance metric, where lower values indicate greater similarity. We applied multiple measures to determine the distance between any pair of vectors for virus and host. We will present the results obtained using the L 2 norm measure. Additional measures that were applied include the L 1 norm and DKL (see Materials and methods), but their use has only a negligible impact on the results, supporting the robustness of the analysis performed hereafter.
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