A small number of assemblies were annotated using our Projection build method. This method was developed to annotate the low-coverage assemblies from the 29 Mammals Project.
This particular annotation method included a step whereby contigs could be joined into 'GeneScaffolds'. This was done where the best reciprocal hit of two contigs in the low coverage genome was matched to one gene annotated on the reference (human) genome assembly. The GeneScaffolds were employed in order to present the full length of the gene models in the low coverage genomes. When contigs were joined with a gap (string of NNNs), any protein coding exons lying over this gap translate as a string of Xs.