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.
Search related documents:
Co phrase search for related documents- end position and Protein sequence: 1, 2, 3
- end position and sequence query: 1
- MERS cov and orf1ab protein: 1, 2, 3, 4, 5, 6
- MERS cov and protein family: 1, 2, 3, 4, 5, 6
- MERS cov and Protein sequence: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52
- MERS cov and sequence identity: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36
- MERS cov and sequence query: 1
- MERS cov and study include: 1, 2, 3, 4, 5, 6, 7
- orf1ab protein and Protein sequence: 1, 2, 3, 4, 5
- protein family and sequence identity: 1, 2, 3, 4, 5
- Protein sequence and query coverage: 1
- Protein sequence and sequence identity: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77
- Protein sequence and sequence query: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15
- Protein sequence and study include: 1
- query coverage and sequence identity: 1, 2, 3, 4
- query coverage and sequence query: 1, 2, 3, 4, 5
- sequence identity and study include: 1
- sequence query and study include: 1
Co phrase search for related documents, hyperlinks ordered by date