Selected article for: "HMMER analysis and nr database"
Author: Stenglein, Mark D.; Jacobson, Elliott R.; Wozniak, Edward J.; Wellehan, James F. X.; Kincaid, Anne; Gordon, Marcus; Porter, Brian F.; Baumgartner, Wes; Stahl, Scott; Kelley, Karen; Towner, Jonathan S.; DeRisi, Joseph L.
Title: Ball Python Nidovirus: a Candidate Etiologic Agent for Severe Respiratory Disease in Python regius
  • Document date: 2014_9_9
    • ID: rb3qdunj_54
    Snippet: Comparative and phylogenetic analyses. ORFs in the viral genome were identified using the Geneious software program (version 6.1; BioMatters). Homologs of predicted protein sequences were detected using the BLASTp tool (version 2.2.25Ï©) to search the NCBI nonredundant protein database (nr) (30) , and by using the HMMER3 alignment tool (version 3.1b1) to search the PFam database (http://hmmer.org) (32) . For HMMER analysis of replicase polyprotei.....
    Document: Comparative and phylogenetic analyses. ORFs in the viral genome were identified using the Geneious software program (version 6.1; BioMatters). Homologs of predicted protein sequences were detected using the BLASTp tool (version 2.2.25Ï©) to search the NCBI nonredundant protein database (nr) (30) , and by using the HMMER3 alignment tool (version 3.1b1) to search the PFam database (http://hmmer.org) (32) . For HMMER analysis of replicase polyprotein, sequence was split into 400-aa sliding windows offset by 60 aa. For sequences with no detectable similarity by those measures, the HHpred homology detection and structure prediction tool (version 2.0) was also used (31) . TMHMM (version 2.0) was used to predict transmembrane domains. The NetNGlyc (1.0) and NetOGlyc (4.0) tools were used to predict N-and O-linked glycosylation sites in protein sequences (33, 34) (http://www.cbs.dtu.dk/services /NetNGlyc/). In cartoons depicting sequence features, all features are to scale and accurately positioned.

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