PRANK (available at http://www.ebi.ac.uk/goldman-srv/prank/prank/) was used for multiple sequence alignments at the codon level.
In contrast to these findings, a number of taxa were analyzed for which multiple sequences were obtained (for at least two markers), but with little or no sequence diversity across the sampled range (based on p-distances, and reported as sequence identity) (Table 1).
The majority consensus sequence, another hypothetical viral sequence that indicates the most abundant nucleotide in the multiple sequence alignment at each position, was built in BioEdit [26].
For further analyses we included only proteins where, after multiple sequence alignment, at most 10 percent of positions were gaps, and no more than 10 percent of any one amino acids sequence contained gaps.
All matching sequences for each exon were aligned using ClustalW (Thompson et al. 1994) to create a multiple sequence alignment at the exon's genome position.
For example, both lin-4 and let-7 target multiple sequence motifs at the 3' UTR of Caenorhabditis elegans hunchback homolog mRNA, hbl-1, and regulate its expression in the ventral nerve cord neurones [ 63].
For each species, in silico predicted motif positions for each TF are shown above the multiple sequence alignment at each promoter when they overlap regions that have evidence of ChIP signal.
Multiple sequence alignments of At MDL1-, MDL1-, Atand At MDL3-like proteins.
Users can search multiple peptide sequences at a time by submitting sequences in FASTA format.
