Selected article for: "cut value and protein sequence"
Author: Yongjun Tan; Theresa Schneider; Matthew Leong; L Aravind; Dapeng Zhang
Title: Novel Immunoglobulin Domain Proteins Provide Insights into Evolution and Pathogenesis Mechanisms of SARS-Related Coronaviruses
  • Document date: 2020_3_7
    • ID: h5ire02h_4
    Snippet: To collect protein homologs, iterative sequence profile searches were conducted by the programs PSI-70 BLAST (Position-Specific Iterated BLAST)(12) and JACKHMMER (15), which searched against the non-71 redundant (nr) protein database of NCBI with a cut-off e-value of 0.005 serving as the significance 72 threshold. Similarity-based clustering was conducted by BLASTCLUST, a BLAST score-based single-linkage 73 clustering method (ftp://ftp.ncbi.nih.g.....
    Document: To collect protein homologs, iterative sequence profile searches were conducted by the programs PSI-70 BLAST (Position-Specific Iterated BLAST)(12) and JACKHMMER (15), which searched against the non-71 redundant (nr) protein database of NCBI with a cut-off e-value of 0.005 serving as the significance 72 threshold. Similarity-based clustering was conducted by BLASTCLUST, a BLAST score-based single-linkage 73 clustering method (ftp://ftp.ncbi.nih.gov/blast/documents/blastclust.html). Multiple sequence 74 alignments were built by the KALIGN (14), MUSCLE(16) and PROMALS3D(17) programs, followed by 75 careful manual adjustments based on the profile-profile alignment, the secondary structure information 76 and the structural alignment. Profile-profile comparison was conducted using the HHpred program (18). 77

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