A.C.Palmenberg

The picornavirus sequences cited in these alignments are those (generally) available in GenBank. The original founding alignments are (were) based on superimposition of virion capsid crystal structure hydrogen-bonding maps from data provided to ACP by Michael Rossmann, in 1994. Since then, the alignments have undergone several iterations. In 2002, Palmenberg & Sgro described extended updates and this is the paper that should be cited, if referencing data from these alignments. In 2005, the aphthovirus and cardiovirus alignments were again revised to include many more genome sequences. Those sequences were collated from The Picornavirus Home Page, a web site maintained by Nick Knowles. Additional sequences were added, as they were found, in GenBank. Incomplete, or partial sequences were avoided unless they contributed information about a unique or unusual strain.

Sequence Alignments Picornavirus RNA genome and protein alignments	A.C.Palmenberg Home Biochemistry UW Graduate School Inst. for Molecular Virology UW-Madison
Palmenberg Alignments 7/14/05 version
The picornavirus sequences cited in these alignments are those (generally) available in GenBank. The original founding alignments are (were) based on superimposition of virion capsid crystal structure hydrogen-bonding maps from data provided to ACP by Michael Rossmann, in 1994. Since then, the alignments have undergone several iterations. In 2002, Palmenberg & Sgro described extended updates and this is the paper that should be cited, if referencing data from these alignments. In 2005, the aphthovirus and cardiovirus alignments were again revised to include many more genome sequences. Those sequences were collated from The Picornavirus Home Page, a web site maintained by Nick Knowles. Additional sequences were added, as they were found, in GenBank. Incomplete, or partial sequences were avoided unless they contributed information about a unique or unusual strain.
Key points: These nucleotide (RNA) alignments have at their foundation, a careful superimposition of crystal structures for all known resolved (encoded) protein structures. Whenever new sequences were added, initially by ClustalW profile-profile fits, the compilation was then edited (Wisconsin Package: SeqLab) to conform with that fit, and to also conform with any other known information concerning protein or RNA conservation for these strains. The RNA alignments maintain open reading frames from which the aligned polyproteins were translated directly. In addition, they respect all known 2D and 3D RNA structural motifs, including 5' and 3' stem elements, 5' pseudoknots, 5' IRES, poly(C) tracts, 3' polyadenylation sites, internal cre elements, etc. The protein alignments for each genus, species or type respect all known proteolytic cleavage sites, enzyme active sites, core protein structures (helices, sheets, turns), and mapped antigenic sites. The RNA alignments (.rna) may be translated directly to produce the respective aligned polyproteins (.p123). File Format: The above links will access text files in MSF format (Wisconsin Package). To access the collective directory of alignment files CLICK HERE. For cardiovirus and aphthovirus alignments, the individual sequences are referenced by their GenBank accession numbers. Conversion tables listing strain designations are in the respective ReadMe files (pdf format). What's Available? In (July 2005) updated RNA and protein alignments were posted for: Cardioviruses (whole genus), FMDVs (select isolates representing the whole species), FMDV-types A, O, C, Asia, and Sat (all available complete genomes). The enterovirus, rhinovirus, etc., alignments may be updated soon, and will follow a similar format. Versions now available (July 2005) for these genera are those updated by ACP& JYS in 2002. Note that for the family alignments, only picorna.p1 and picorna.2CP3 files can be formed. The remainder of the polyproteins, and the 5' and 3' RNA elements are not (always) homologs among the genera so they cannot be usefully aligned.
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