Though these traditional tests are Erythromycin Ethylsuccinate highly specific and have been used for decades, they have major limitations. In particular, detection of novel, divergent, elusive, or low copy number viral genes within a Orientin complex host genetic background can be quite difficult using traditional tools such as PCR, conventional sequencing technologies, and even DNA microarrays. These li mitations can be overcome by deep sequencing primary human samples, such as tissue, cerebral spinal fluid, bronchial or nasal lavage, and stool. Samples from non-sterile locations may contain nucleic acid from numerous commensal organisms, and the direct sequencing of all nucleic acid species of a specimen can elucidate the specimen��s metagenome, i.e., the sequences derived from all the organisms present in the specimen. Thus, shotgun metagenomic sequencing for viral discovery necessitates identification of specific RNA or DNA sequences in the context of a complex and potentially unknown background of irrelevant nucleic acid. Due to the decreasing cost and increasing throughput of secondgeneration sequencing technologies, deep sequencing of metagenomes and metatranscriptomes has become a critical tool for the identification of novel or divergent viruses that are difficult to detect by other methods. For example, massively parallel sequencing has been used to discover a variety of novel viruses, from a novel member of the Bornaviridae family in birds, to novel members of the Arenaviridae family in snakes. Massively parallel sequencing can help overcome the problem of detecting pathogens present at vanishingly low amounts; traditional Sanger sequencing approaches will not provide ample sequencing depth to detect the pathogen because the proportion of metagenomic data deriving from a target pathogen may be on the order of one in one hundred thousand reads or lower. A single deep sequencing experiment can now generate billions of sequencing reads, each of which is hundreds of nucleotides long.As generating viral sequence from metagenomes becomes more commonplace, there still remains the bioinformatic challenge of actually identifying those sequences, especially when the virus present is only distantly related to known viruses.