Prior to pairwise alignment, contigs assembled from the unmapped DNA reads were sorted by size and only contigs greater than 500 bases were aligned (n = 42,086).
Overall, 1,253,655 bases were aligned with 99.87% identity.
The first 41 bases were aligned to the rat reference genome using the Gerald program.
The average DNA coverage was 106× as ∼21 million DNA reads, with average length of 83 bases were aligned to the coding sequences.
The remaining bases were aligned to the Genbank nonredundant protein database, which resulted in 9.48% of all BESs having a hit to coding sequences.
A total of 817,470,439 reads (59,643,456,282 bases) were aligned to approximately 97% of the reference genome (53,783,377,648 bases were uniquely mapped), resulting in an average of 24.7X sequence coverage of the horse's genome (Additional file 3, Table S2).
Reads that passed quality control (more than 90%% bases had less than 1%% sequencing error; no ambiguous bases) were aligned to the mouse genome (Mus_musculus.GRCm.38.72) with corresponding gene model annotation (Mus_musculus.GRCm38.72.gtf) by TopHat 2.0.6 [ 16].
Subsequently the H. sapiens, R. norvegicus, M. musculus and S. cerevisiae based sub-network were aligned and integrated in order.
All Brassica napus gene sequences matching a particular Arabidopsis candidate gene were aligned and based on these alignments gene-specific oligonucleotide pairs were developed.
These tags were aligned and identified based on two reference genomes, Ensembl Sus scrofa 10.2.68 and the UniGene database.
