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Trimmed sequences, as well as un-trimmed ones, were mapped to the reference sequence (ref_seq).
While in the "transcriptome + genome" mapping mode, reads were first mapped to a reference transcriptome, and then the unmapped ones were mapped to the reference genome.
Amino acid sequences were used for assignment of KO identifiers to the gene products from each species by the KAAS system and the KO assigned ones were mapped to the KEGG modules.
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Observing the projection in Figure 2, two samples ("Tempio Rotondo" and itNM1) are seen to fall very close to known marbles (Pentelic and Piastra Ravaccione, respectively), while all the remaining ones are mapped onto "empty" regions of space.
Mapping analysis showed, however, that Gypsy elements are more redundant than Copia ones, being mapped by 28,884,342 and 24,725,640 reads, respectively.
Irrelevant concepts are filtered out by semantic types and the relevant ones are mapped to a target terminology used to encode the database.
All distorted markers but one were mapped on the consensus map and more than half clustered mainly into two linkage groups (group 2 and 8) with the others scattered across eight linkage groups.
Of the 440 genes and ESTs located on the map, a total of 110 genes have previously been mapped either by linkage or physically and all of these except one were mapped to the expected chromosome.
Two important ones are mapping between coordinates and modeling of fluid flow complex physics.
When multiple probes from one platform were mapped to one probe from the other platform, a one to one probe pair was randomly selected.
Seventy-one species were mapped by taxonomic identifiers, 27 by species name.
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