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Once the PCR-RFLP tests (see below) had been developed, more sequences were obtained for the variants initially underrepresented.
More sequences were duplicated than expected, but this is possibly an artefact of the SMARTer amplification process.
Rarefaction analysis yielded an asymptotic curve at the distance level of 0.2, meaning that if more sequences were analyzed, new phyla would not have been detected (Figure 7A).
"In the last 10 weeks, more sequences were added to the GenBank database than in the first 10 years of genomics," reveals Robbins.
The second misconception can also be corrected by pointing out that "straight" lines are often African clades of which subclades have not been described (for example H clade is the one with most subgroups as it represents mostly European sequences, a very well-researched group, see Fig. 1), if more sequences were available, the L clades could be substantially expanded by many added nodes.
Two months after this initial annotation comparison, about 350 more sequences were indeed labeled as sHSP in UniProt.
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Philippe, H. et al. Resolving difficult phylogenetic questions: why more sequences are not enough.
Alternatively, because 20 times more sequences are available than for EBOV, we selected years with at least ten strains of one category to reduce the artefactual effects derived from sequencing uncertainty.
However, the difficulty in finding the similar regions between two or more sequences is very hard due to the size of the existing sequence involved.
We have developed a method for analysing the apparent stability of conserved sites as more sequences are discovered and reported.
This becomes even more apparent as more sequences are used for the tree inference.
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