In a few cases (ND1, ND2, ND5 and COX2), relying on tBLASTn alignments was insufficient since coding sequences could not be properly determined without an additional analysis of ORF.
Several studies showed that potential ncRNAs in genomic sequence have altered their primary sequence while maintaining their secondary structure and the sequence-based alignments are insufficient to represent the RNA structure across related species (Torarinsson et al., 2006, 2008).
Next-generation sequencing results from bead-based aptamer libraries have demonstrated that traditional DNA/RNA alignment software is insufficient.
Nonetheless, we have implemented an analogous extension, aware that the induction we use constitutes a loss of optimality where alignment space is insufficient.
We inferred two phylogenetic trees with different repertoires of subfamilies, as the inclusion of both the MAGI and CACNB subfamilies in a single dataset results in a short alignment, that is insufficient for reliable tree inference.
The amount of data at each site of an alignment is considered to be insufficient to allow an independent estimation of ω for individual sites.
A similar function could be attributed to the P. brasiliensis pct gene, although alignment data are insufficient to identify which cation this protein transports.
Ideally, mapping time is largely spent on the matching and validation of true alignments, but if the seed weight is insufficient, the examination of random hits will dominate the running time.
Reference-guided alignment was utilized in this study because a 1x genomic coverage is insufficient for de novo genome assembly.
