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In fact, the profile-based search method appeared to be less sensitive than all BLAST-based search methods – nucleotide, protein or translated (Table 1 and Table 2).
Such leaderless mRNAs with a very short 5′-UTR were also found to be efficiently translated (table 2) (Krishnan et al. 2010).
The six remaining ORFs contain smaller fragments of known genes that are from the complementary DNA strand and/or from ribosomal RNA genes that are not normally translated (table 4), and none is predicted to contain a transmembrane domain.
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Open-reading frames (ORFs) of length more than 50 (amino acids) were translated using National Center for Biotechnology Information translation table 4 and compared with the databases using BlastX (Gish and States 1993).
Thirty-seven particompletedomplethistranslatedlated version (Table 2).
In contrast, after applying the mophosemantics phase 87.84% of the simple terms are translated (see Table 8).
Many of the wholly translated exons (Table 2) have factor values close to thirty; the mean average being 36.
None of the variants caused translational frameshifts or nonsense codons and three were synonymous (i.e. maintaining the amino acid sequence of the translated protein; Table 2).
In addition to the sign attribute, the Input object is assigned an SBO term that further specifies the semantics based on subtype translated (see Table 4).
Four of the 11 were deemed by that study as "not expressed" (no detectable mRNA) and the other 7 were classified as "not translated" (supplementary table S3, Supplementary Material online).
Our matching algorithm translates the table data to a set of class objects by comparing column names in the table data and parameter names in the class definition.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com