Extension of the viral ecology in humans using viral profile hidden Markov models.
Ontology highlight
ABSTRACT:
SUBMITTER: Bzhalava Z
PROVIDER: S-EPMC5774701 | biostudies-literature | 2018
REPOSITORIES: biostudies-literature
Publications
Extension of the viral ecology in humans using viral profile hidden Markov models.
Bzhalava Zurab Z Hultin Emilie E Dillner Joakim J
PloS one 20180119 1
When human samples are sequenced, many assembled contigs are "unknown", as conventional alignments find no similarity to known sequences. Hidden Markov models (HMM) exploit the positions of specific nucleotides in protein-encoding codons in various microbes. The algorithm HMMER3 implements HMM using a reference set of sequences encoding viral proteins, "vFam". We used HMMER3 analysis of "unknown" human sample-derived sequences and identified 510 contigs distantly related to viruses (Anellovirida ...[more]
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