Determination of gene sequences in silico. (1) Individual data sets were assembled into contigs using Velvet. (2) BLAST searches for genes of the nAChR-pathway were carried out with a high cutoff (expect value = 1E-10) to identify contigs highly similar to the target genes. (3) Reads were individually mapped (using Bowtie) to high similarity contigs. (4) All paired-reads for which at least one read mapped to a contig (in Step- 3) were identified and binned using a custom Java program. (5) De novo assembly of Step- 4 sequences was performed using Velvet. (6) Iteration of Steps 3-5 was performed until the iteration resulted in no additional reads being mapped to the contig of interest.
Romine et al. BMC Genetics 2013 14:55 doi:10.1186/1471-2156-14-55