Therefore, it is predicted that if translated, these sequences will result in truncated proteins.
We translated these Z. celata sequences into amino acid sequences and aligned them with previously characterized, complete T2-RNase amino acid sequences from 12 plant families.
The Translate program (http://web.expasy.org/translate/, last accessed May 27 , 2014 was used to translate nucleotide sequences.
These translated sequences were fetched as amino acid sequences from stop codon to the next stop codon, stored in a database as a six-frame translated genome database.
This search produced hits indicating high similarity (E-value 10-88 to 10-30) between the deduced SmTRC1-ORF translated sequence and translated sequences from genomes of such diverse animals as Strongylocentrotus purpuratus, Ciona intestinalis, Danio rerio and Aedes aegypti.
The search against fungal genomes produced hits indicating moderate similarity (E-values 10-16 to 10-4) betheen the deduced SmTRC1-ORF translated sequence and translated sequences from the genomes of e.g. Rhizopus oryzae, Coprinopsis cinerea and Phanerochaete chrysosporium.
Thus, if a tested genotyping approach was not designed to account for ambiguous nucleotide positions, all possible combinations of amino acid sequences were output and a worst-case scenario approach was employed whereby if one of these translated sequences was predicted as CXCR4-using, the genotyping call for the original sequence was taken as X4.
Annotated protein sequences of these enzymes from apicomplexans and other major taxonomic groups (i.e., plants, bacteria, fungi and animals) were used as queries to repeatedly search the nucleotide or translated protein sequences in these databases using TBLASTN and BLASTP algorithms [59], respectively.
The translated protein sequences containing these LCRs were aligned using Muscle (Edgar 2004).
We used the translated protein sequences from these intergenic ORFs and analyzed them using InterPro Scan via EXPASY.
