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It was therefore necessary to perform this alignment manually.
To perform this alignment we followed the same strategy used to obtain the non-redundant alignment using CAPs.
The nucleotide blast program (blastn) of NCBI's 'Basic Local Alignment Search Tool' (BLAST) [ 37] was used to perform this alignment, with cutoffs for expected score set at below 0.1 and percent identity set at above 60% of the length of the hairpin sequence.
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It was not possible to measure the time spent performing this alignment since it was part of the evolution process of VCM.
We introduce here a method to perform this assignment using both multiple alignments of 3'UTR regions and EST mapping of polyadenylation sites.
The multiple alignments were concatenated, and phylogenetic reconstruction was performed on this alignment.
Figure 3 presents the results of phylogenetic analyses performed on this alignment.
The automated process we use to perform the alignment of spectra is explained in Appendix 1.
In order to perform the alignment, approximation is required.
Note that this approach requires performing the alignment of all possible combinations, and it was only intended for benchmarking.
Since we already performed this step during face alignment as discussed in Section 3.2, we do not use the rotation-invariant version of the SURF descriptor.
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