PASA first summons BLAT[29] to align the CDSs to the genome and then validates each alignment by requiring a minimum 95% sequence identity over at least 90% of the gene length.
PS relies on a global alignment as obtained by ClustalW [23] to identify the conserved blocks, while the more refined procedure of PG requires an alignment strategy, such as Dialign [22] that explicitly annotates aligned and unaligned regions.
The weight is constructed from the vector fields by requiring local alignment of the mesh with the fields and by prescribing local length scales.
For this reason, as well as the presence of pseudogenes, we further filter our set of alignments by requiring each alignment to cover at least 80% of the subject gene.
While a second, allele-aware alignment increases accuracy at predicted heterozygous sites, these modest gains, still accompanied by a high rate of false discovery, require an additional alignment.
The sequences were filtered further, by requiring at least a 300 bp alignment length (Step 2.3, fig. 1) and more than 80% ID along that alignment (Step 2.4, fig. 1), which is a standard benchmark for paralogs in salmonid species (Koop et al. 2008; Leong et al. 2010).
Our pure sequence-based approach is different from other methods that use sequence alignments (like the functional-residue-clustering (FRC) method) 31 that lead to abstract data by defining amino acid alphabets and require a joint alignment including subfamily members.
Even when one requires a nucleotide alignment, the approach of translation, MSA, followed by back translation seems likely to yield better results.
This calculation is very simple and requires only an alignment length and RMSD as calculated by the method, which all of the methods tested here report.
But, for me, that requires a special alignment of the planets.
