Selected article for: "Neighbor Joining NJ method and NJ method"
Author: Chang Liu; Ze Chen; Wenyuan Shen; Deshui Yu; Siyu Li; Yue Hu; Haishuo Ji; Wenjun Bu; Qingsong Wang; Shan Gao
Title: Complemented palindrome small RNAs first discovered from SARS coronavirus
  • Document date: 2017_9_7
    • ID: g55d5ijx_16
    Snippet: Using the software bowtie v0.12.7 with one mismatch, we aligned all the cleaned sRNA-seq reads to viral 206 genome sequences and obtained alignment results in SAM format for detection of siRNA duplexes using the 207 program duplexfinder [7] . Statistical computation and plotting were performed using the software R v2.15.3 208 with the Bioconductor packages [16] . The orf3b gene from human betacoronavirus (GenBank: 209 DQ497008.1), its 20 homologo.....
    Document: Using the software bowtie v0.12.7 with one mismatch, we aligned all the cleaned sRNA-seq reads to viral 206 genome sequences and obtained alignment results in SAM format for detection of siRNA duplexes using the 207 program duplexfinder [7] . Statistical computation and plotting were performed using the software R v2.15.3 208 with the Bioconductor packages [16] . The orf3b gene from human betacoronavirus (GenBank: 209 DQ497008.1), its 20 homologous sequences from bat betacoronavirus and nine homologous sequences from 210 civet betacoronavirus were aligned using ClustalW2 (Supplementary file 2) . After removal of identical 211 sequences, the orf3b gene from human betacoronavirus, eight homologous sequences from bat 212 betacoronavirus and two homologous sequences from civet betacoronavirus were used for phylogenetic 213 analysis. Since these homologous sequences had high identities (from 85.16% to 99.78%) to the orf3b gene 214 from DQ497008, the Neighbor Joining (NJ) method was used for phylogenetic analysis. 215 216

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