Author: Jabado, Omar J.; Liu, Yang; Conlan, Sean; Quan, P. Lan; Hegyi, Hédi; Lussier, Yves; Briese, Thomas; Palacios, Gustavo; Lipkin, W. I.
Title: Comprehensive viral oligonucleotide probe design using conserved protein regions Document date: 2007_12_13
ID: xfzhn1n1_14
Snippet: All coding nucleic acid sequences that were not part of a Pfam-A alignment were extracted. In this step, the most conserved regions within homologous genes were identified for probe design. Sequences were clustered at the protein level with CD-Hit, using a similarity threshold of 80%. All sequence clusters were subjected to a MEME motif search (34) using the following parameters: motif width of 20, zero or one motif allowed per sequence, a minimu.....
Document: All coding nucleic acid sequences that were not part of a Pfam-A alignment were extracted. In this step, the most conserved regions within homologous genes were identified for probe design. Sequences were clustered at the protein level with CD-Hit, using a similarity threshold of 80%. All sequence clusters were subjected to a MEME motif search (34) using the following parameters: motif width of 20, zero or one motif allowed per sequence, a minimum of two sequences per motif. Three motifs were selected for each sequence cluster. The underlying nucleic acid sequence extracted for each protein motif was used for probe design.
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