Searching for new ORFs Sample Clauses

Searching for new ORFs. Close inspection of the Refseq+22 compendium revealed some critical missing annotations. As an example, DNA polymerase was missing in the genome of Staphylococcus phage G1 (NC_007066, Caudovirales, Myoviridae), whilst this enzyme has been shown to be conserved in the T7-phages replication modules (Xxxxxx and Xxxxx, 2006). Similarly, the capsid protein pVIII sequence is missing in the genome of the Human adenovirus D (AC_000006.1, Adenoviridae), whilst X. Xxxxxxx (in Xxxx et al., 2011) showed that this enzyme is conserved in all Adenoviridae genera. We therefore decided to search if bona fide protein coding genes have been missed in intergenic sequences of RefSeq+22. For the bioinformatics analyses, we mainly used EMBOSS applications found here: xxxx://xxxxxx.xxxxxxxxxxx.xxx/docs/ After extraction of intergenic sequences using maskfeat, we used getorf to search for intergenic open reading frames (IgORFs) with a specified minimum size of 90 nucleotides between two STOP codons (taking into account the genetic code specific for each virus). We obtained 188,818 putative IgORFs. To focus on the most probable IgORFs, we searched IgORF similarities with sequences contained in the following databases (using blastp for nr, env and RefSeq Viral proteins, and using rpsblast for CDD):
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