The modularization enforced by componentization pervades throughout the toolkit and is reflected in assembled codes.
We assembled coding sequence data from 55 animal species, including 27 species of platyhelminth.
It has been shown that the standard genetic code is preferential to randomly assembled codes for its ability to reduce the effects of errors in protein translation.
We used the mapping algorithm in the CLC Genomics Workbench v6.5.1 (CLC bio, Cambridge, MA) to map the reads to the assembled coding sequences.
When searching for themes, we assembled codes into potential themes and considered how these could be combined as sub-themes from which overarching themes could be derived.
For comparisons to known serpins, assembled coding sequences were scanned against known protein entries in GenBank using the BLASTx or BLASTp homology search program.
The fully assembled coding regions of the variants generated from both patients were compared to previously described PARV4 variants (n = 18 viral proteins 2/1 and n = 19 nonstructural sequences) (Table 2).
The protein-coding part of DNA is copied, or transcribed into an intermediate molecule called RNA that has the same sequence as that part of the DNA, but in the cell is grabbed by specific organelles called "ribosomes," which translate the code by assembling the code-specified amino acids, one by one, in the same order as the nucleotide code copied from DNA, into the protein being specified.
Using this approach, we predicted coding regions in 5213 out of 5229 assembled protein-coding transcripts at least 100 amino acids long (99.7 %), versus just 7 out of 660 intergenic transcripts (1.1 %) and 11 out of 474 antisense transcripts (2.3 %).
This approach, with verification in two independently sequenced individuals for each species, minimized assembly artifacts to ensure that only well assembled protein-coding sequences were included into subsequent analyses.
