Author: S. Willis; J. Masel
Title: Gene birth contributes to structural disorder encoded by overlapping genes Document date: 2017_12_6
ID: 9w2wjiik_29
Snippet: We constructed a pHMMer (http://hmmer. org/) database including all overlapping regions, nonoverlapping genes and their frameshifted controls. After an all-against-all search, sequences that were identified as homologous, using an expectation value threshold of 10 −4 , were provisionally assigned the same homology group ID. These provisional groups were used to determine which gene birth events were unique. Two pairs were considered to come fro.....
Document: We constructed a pHMMer (http://hmmer. org/) database including all overlapping regions, nonoverlapping genes and their frameshifted controls. After an all-against-all search, sequences that were identified as homologous, using an expectation value threshold of 10 −4 , were provisionally assigned the same homology group ID. These provisional groups were used to determine which gene birth events were unique. Two pairs were considered to come from the same gene birth event when both the ancestral and the overlapping sequence were classified as homologous. We also used published phylogenetic analysis to classify the TGBp2/TGBp3 overlap as two birth events (one occurring Virgaviridae, the other occurring in Alphaand Betaflexiviridae) [27] .
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