Author: Ramya Rangan; Ivan N. Zheludev; Rhiju Das
Title: RNA genome conservation and secondary structure in SARS-CoV-2 and SARS-related viruses Document date: 2020_3_28
ID: kjeqdse5_28
Snippet: Three alignments for SARS-related viruses were prepared: 1. SARSr-MSA-1 was generated by re-aligning the sequences curated by Ceraolo and Giorgi 10 with MUSCLE 33 using default alignment settings, excluding all non-reference genome copies of the SARS-CoV-2 sequence and excluding MERS sequences JX869059.2 and KT368829.1. 2. SARSr-MSA-2 was generated by downloading the MSA provided by BLAST for the top 100 complete genome sequences closest to the S.....
Document: Three alignments for SARS-related viruses were prepared: 1. SARSr-MSA-1 was generated by re-aligning the sequences curated by Ceraolo and Giorgi 10 with MUSCLE 33 using default alignment settings, excluding all non-reference genome copies of the SARS-CoV-2 sequence and excluding MERS sequences JX869059.2 and KT368829.1. 2. SARSr-MSA-2 was generated by downloading the MSA provided by BLAST for the top 100 complete genome sequences closest to the SARS-CoV-2 reference genome. 3. SARSr-MSA-3 was generated by obtaining all complete betacoronavirus genome sequences available from the NCBI database, removing mutually similar sequences using a 99% cutoff with CD-HIT-EST 34 , and computing an MSA with Clustal Omega 35 using default settings.
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