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This may account for some of the low similarity values observed in these comparisons as this type of refinement is observed in numerous places across the different atlases in, for example, the cerebellum (e.g. ICBM vs. H-O), thalamus (e.g. T&G vs. ICBM), and cerebral cortex (e.g. the cingulate cortex in LPBA40 vs. AAL), to name only a few.
We speculated that the effectiveness of the shuffling algorithm correlates with the size of the MSA; those MSA containing fewer sequences benefiting more from this type of refinement.
The first type of refinement was to re-annotate genes in iKF1028 - based on literature evidence and BLAST searches - that have been improperly annotated.
In another type of refinement of CDS co-ordinates using GSSPs mapping to UTRs, we found 8 instances of N-terminal in-frame extensions using peptides that mapped to 5′ UTR of genes and 5 cases of C-terminal extensions with the aid of peptides mapping to 3′ UTR of genes (Additional file 10: Table S6).
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The first type of refinements is the one set by the tool itself.
Another type of refinements should take place in order to optimize the size, the speed and sometimes (depending on the used tool) power consumption.
Some other types of refinements have been studied in the recent papers [12] and [5].
Two types of refinements are considered, namely, a predicate refinement and a refinement based on selected sets of parameterized inputs as is illustrated in details in Section 5. A high-level overview of the algorithm is provided below and the detailed algorithm is given in the following subsection.
Another type of annotation refinement was based on gap analyses, which pinpointed reactions for which the gene products involved were missing.
It was more a case of refinements on existing technology.
Along with the information that the type 0 object u refines both of the elements of type 1, this gives a complete recursive definition of the notion of refinement of a type n set by a type n + 1 set.
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