Selected article for: "NCBI database and reference database"
Author: Rahaman, Jordon; Siltberg-Liberles, Jessica
Title: Avoiding Regions Symptomatic of Conformational and Functional Flexibility to Identify Antiviral Targets in Current and Future Coronaviruses
  • Document date: 2016_11_9
    • ID: pygykil7_8
    Snippet: Protein sequences were identified by individual BLAST searches with MERS-CoV (Taxonomy ID: 1335626) proteins ORF1ab (YP_009047202.1; polyprotein), S protein (YP_009047204.1), M protein (YP_009047210.1), E protein (YP_009047209.1), and N protein (YP_009047211.1) against coronaviruses. BLAST searches of the ORF1ab protein were performed, using start and end positions as detailed in the ORF1ab NCBI Reference Sequence file, against the refseq_protein.....
    Document: Protein sequences were identified by individual BLAST searches with MERS-CoV (Taxonomy ID: 1335626) proteins ORF1ab (YP_009047202.1; polyprotein), S protein (YP_009047204.1), M protein (YP_009047210.1), E protein (YP_009047209.1), and N protein (YP_009047211.1) against coronaviruses. BLAST searches of the ORF1ab protein were performed, using start and end positions as detailed in the ORF1ab NCBI Reference Sequence file, against the refseq_protein database. The sequences retrieved from the BLAST output maintained the following cutoff: >30% sequence identity and >50% coverage relative to MERS-CoV sequence query. The 30% sequence identity and 50% query coverage cutoff strikes a balance between alignment quality and at least 10 sequences for most protein families. NSP1 (YP_009047202.1; 1-193), NSP2 (YP_009047202.1; 194-853), NS3 (YP_009047205.1), NS4A (YP_009047206.1), NS4B (YP_009047207.1), NS5 (YP_009047208.1), ORF8b protein (YP_009047212.1), and NSP11 (YP_009047203.1; 4378-4391) are not included in this study due to <10 BLAST hits.

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