We also found two unique DLPs (named navitricin-1 and -2) in the N. vitripennis genome, which possess 8 cysteines with an identical alignment pattern to the family III members of fungal DLPs [ 32].
We removed short reads mapped with quality alignment scores of zero (Q0), which correspond to reads mapped to two or more locations on the reference genome with identical quality alignment scores.
After PCR amplification and sequencing of DNA from selected regions of the COI gene and ribosomal ITS region, we found identical alignment of sequences from Ao38 cells and High Five (T. ni) cells, and nearly identical alignment with sequences from T. ni larvae, as well as with T. ni sequences in the BOLD database [ 3, 4].
Second, some reads may have nearly identical alignment to locations in the gene and pseudogene, and their mapping is often determined by the location with the least error in alignment.
For benchmarking the precision of contact prediction methods, we use the same set of 150 Pfam families with ≥ 1000 sequences and high-resolution structures (≤ 1.9 Å) with identical input alignments as used in the PSICOV (Jones et al., 2012) method.
Sequence read alignment performed with an alternative aligner, Bowtie, yielded identical alignments for the large majority of reads and indistinguishable results in all downstream analyses.
Finally, Fosmid sequences were aligned to assembly scaffold sequences using BLASTN with parameters tuned for long, nearly identical alignments (WU-BLASTN [04-May-2006] W=13 M=1 N=-3 Q=3 R=3 kap S=1000 S2=1000).
The alignments used for the calculations of Table 1 and illustrated in Fig. 1 are rigorous because they consider many sequences and almost identical alignments are obtained with a variety of methods that all take into account residue similarities as well as identities.
As they all use CAP3 with identical parameters for alignment, the consensus sequences are very similar, with the average identity of each contig consensus sequence to the original FL-cDNA being over 99%.
