Author: Anna Shcherbina; Darrell O. Ricke; Nelson Chiu
Title: Evaluating performance of metagenomic characterization algorithms using in silico datasets generated with FASTQSim Document date: 2016_3_31
ID: csokkcqq_9
Snippet: MetaPhlAn[9] relies on unique clade--specific marker genes identified from 3000 reference genomes. 53 The Livermore Metagenomic Analysis Toolkit (LMAT) exploits genetic relationships between different 54 organisms by pre--computing the occurrence of each short sequence across the entire reference 55 database and storing the evolutionarily conserved sequence patterns [10--12] . MetaCV translates 56 nucleotide sequences into six frame peptides, whi.....
Document: MetaPhlAn[9] relies on unique clade--specific marker genes identified from 3000 reference genomes. 53 The Livermore Metagenomic Analysis Toolkit (LMAT) exploits genetic relationships between different 54 organisms by pre--computing the occurrence of each short sequence across the entire reference 55 database and storing the evolutionarily conserved sequence patterns [10--12] . MetaCV translates 56 nucleotide sequences into six frame peptides, which are then decomposed into k--mers. The k--mer 57 frequency is computed in a protein--reference database and used to assign k--mer weights [13] . Finally, 58
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