Author: Rose, Rebecca; Constantinides, Bede; Tapinos, Avraam; Robertson, David L; Prosperi, Mattia
Title: Challenges in the analysis of viral metagenomes Document date: 2016_8_3
ID: x3u9i1vq_29
Snippet: Although these approaches are less accurate than BLAST searches, PHYMMBL (Brady and Salzberg 2011) combines PHYMM and BLAST and outperforms either one on its own. Alignment-free comparison approaches, for example, based on dinucleotide frequencies, codon usage patterns, or small but conserved regions of family wide ubiquitous genes, may be more robust to the limitations of the database than sequence similarity searches. These features may also re.....
Document: Although these approaches are less accurate than BLAST searches, PHYMMBL (Brady and Salzberg 2011) combines PHYMM and BLAST and outperforms either one on its own. Alignment-free comparison approaches, for example, based on dinucleotide frequencies, codon usage patterns, or small but conserved regions of family wide ubiquitous genes, may be more robust to the limitations of the database than sequence similarity searches. These features may also reduce the computation required and highlight evolutionary relationships otherwise obscured by high sequence variability.
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