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For BLASTER, we kept matches with E-value below 10−300, a length exceeding 100 bp and an identity exceeding 90% (parameters "-E 1e-300 -L 100 -I 90").
Sequences with an identity exceeding 99% were pooled into one contig (Sequencher 4.8) and the consensus sequence was created.
Accordingly, a complete transcript was only matched to a gene if both the first and the second exon showed an identity exceeding 99%.
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Only sequences with a reciprocal best hit with a percentage identity exceeding 85%, an e value below e−, and an alignment of more than 200 bp were retained as homologous unigenes.
Unigenes with a percentage identity exceeding 95% with mapped SNP flanking sequences were retained for the next step.
Thus, we choose the highest mode of identity distribution as a reference to compute the unilateral P-values of our tests, which quantified the probability of each candidate to have a nucleotidic identity exceeding 95.63%, while accounting for the size of the alignment (fig. 2).
For any pair to be reported as near-identical, we required an HSP of at least 50 bp and a pairwise sequence identity exceeding 75%.
Upon inspection only one was found to share a protein sequence identity exceeding 50% with any known alphaproteobacteria gene, sharing 71% protein sequence identity to virD4 (Arad_15020) of A. rhizogenes K84.
UCRs are more strongly conserved than sequences encoding identical proteins, and exhibit sequence identity exceeding essentially all known cis-regulatory sequences.
For PALS, we used the default parameters: identity exceeding 94% and a length of more than 400 bp (parameters "-length 400 -pctid 94").
An arbitrary cut-off of sequence identity exceeding 99% was used to identify possible allelic variation.
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CEO of Professional Science Editing for Scientists @ prosciediting.com