At the protein level, the maximum percent identity difference was 1.4% (3/209): 7 haplotypes of sequences were detected (data not shown).
This output was summarized according to the total number of alignments per species, mean, median, and maximum percent identity, mean, median, and maximum length of match, and mean and median E-value (Additional file 1: Tables S3 and S5).
2. Maximum percent identities and e-values were obtained by blastx against the An.
The maximum nucleotide percent identity difference between the 46 sequences was low (0.96%; 6/627).
The maximum e-value of 1e-5, minimum percent identity of 60, and minimum alignment length of 30 were applied as the parameter settings in the analysis.
The maximum E-value of 1 e − 5, minimum percent identity of 60, and minimum alignment length of 50 pb were applied as the parameter settings in the analysis.
Assembly of reads in contigs and singletons to estimate the redundancy of the ESTs, get the consensus sequences of the redundant ones, and obtain the unigene set was made with tgicl [ 51], using the following default parameters: 30 bases minimum overlap length, 94% minimum percent identity for overlaps, and 30 bases maximum length of unmatched overhangs.
EST assembly was processed using the TGI Clustering tools (TGICL, http://compbio.dfci.harvard.edu/tgi/software) using the default parameters (minimum percent identity for overlaps: 94, minimum overlap length: 30 bp, maximum length of unmatched overhangs: 30), generating unigenes and singletons.
In a MUMmer alignment of the genomic sequences, the minimum percent identity between the two strains was 76.66% and the maximum was 99.07%, with an overall average of 93.62%.
Clustering was performed using the following variable parameters: minimum percent identity for overlaps (94%), minimum overlap length (30 nt) and maximum length of unmatched overhangs (30 nt).
For the clustering step, we used a minimum percent identity for overlaps (p) of 94, a minimum overlap length (l) of 30, a maximum length of unmatched overhangs (v) of 30.
