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Finally, the mutations predicted to change amino acids were analyzed by using the annotated version of Gmax_189.
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Additional searches for MHC genes were performed by using the "Annotate from Database" function in Geneious, which used a BLAST-like algorithm to match known tuatara MHC sequences from cDNA (Miller et al. 2005, 2006) to the BAC clone sequence.
Table 1 Comparison by using the manually annotated sequence.
Each variant called by RAREVATOR is annotated by using the VEP annotation combined with GENCODE, GAD and RegulomeDB annotation.
The KEGG analysis were performed by using the KEGG annotating function of Blast2GO software, and the annotated KEGG pathways were further manually classified according to the published KEGG pathway lists (http://www.genome.jp/kegg/pathway.html).html
Selected genomes were annotated by using the MicroScope annotation and comparative genomics platform (19 ).
All protein-coding genes were then annotated by using the RAST annotation pipeline http://rast.nmpdr.org/[ 23].
After importing documents to the project, they can be automatically annotated by using the available concept and relation annotation services.
Human sequence was used as the baseline and annotated by using the exon/intron information available at Ensembl genome browser.
From the 75,618 unigenes assembled nearly 67%% was annotated by using the NR database.
All RRA loci were annotated by using the web interface of VEP.
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