2.4. Gene Annotation and Sequence Analysis

Manual assembly of the sequences obtained was performed by employing Clustal X 1.83 in contrast to T. trichiura complete mt genome sequence. The analysis of the open reading frames was executed by selecting invertebrate mitochondrial code using Open Reading Frame (ORF) Finder (http://www.ncbi.nlm.nih.gov/gorf/gorf.html) and subsequently comparison was done with mt genome sequences of other enoplids [24,29,30]. Genes were translated individually to get amino acid sequences by selecting invertebrate mitochondrial code in the software MEGA5 [31]. The alignment of the resulting amino acid sequences was performed against amino acid sequences of mt genomes of other nematodes utilizing Clustal X 1.83. For homologous genes, percentage of amino acid identity was also calculated on the basis of pairwise comparison. Codon usage was determined on the basis of relationships between nucleotide composition, codon families, and amino acid occurrence where the genetic codes are split into rich AT, GC, or neutral codons. Secondary structures of tRNA genes were identified to get rRNA genes by using the ARWEN tool (http://mbio-139 serv2.mbioekol.lu.se/ARWEN/) [32] and visual inspection [33].