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_3
Snippet: The Protein Families Database (Pfam) (23) is a repository of hand curated protein multiple alignments and Hidden Markov Models (HMMs) across all phylogenetic kingdoms. HMMs are probabilistic representations of protein alignments that are well suited to identifying homologies (24, 25) . Beginning with the Pfam database as a foundation, we established a tiered method for creating viral probes that uses all sequence information available for viruses.....
Document: The Protein Families Database (Pfam) (23) is a repository of hand curated protein multiple alignments and Hidden Markov Models (HMMs) across all phylogenetic kingdoms. HMMs are probabilistic representations of protein alignments that are well suited to identifying homologies (24, 25) . Beginning with the Pfam database as a foundation, we established a tiered method for creating viral probes that uses all sequence information available for viruses. Our method for probe design employs protein alignment information, discovered protein motifs, nucleic acid motifs and finally, sliding windows to ensure near complete coverage of the database.
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