PSI-BLAST is much faster than HMMer because it uses an index of k-mers to find short matches, and it only considers alignments around regions that contain two such short matches.
Ortheus considers alignments of human, chimpanzee, orangutan, and rhesus macaque, but it does not explicitly model context-dependent substitution rates.
After that, the final tool path is modified by considering alignment error, tool radius error and squareness error.
Therefore, the method can be considered alignment independent, and the use of the signal peptide feature is applicable even where sequence alignment deteriorates considerably.
These putative proteins share approximately 25-50% sequence identity to human GPCR pathway proteins when considering alignment lengths >100 aa.
A suggested way to solve this problem is to consider alignment as a random variable, a strategy developed into the statistical alignment procedure [ 49, 50].
First, it may be interesting to consider alignment of weighted PPI networks with weights representing, for instance, experimental evidence of interaction existence.
In the second step, the candidate set was converted to the final SNP set using Bayes model, considering alignment quality and read support.
In this study, we use this idea to compare the most widely-used methods for pairwise structural alignment, in addition to considering alignment accuracy relative to other annotation sources: DSSP structural classes (Kabsch and Sander, 1983) and solvent accessibilities.
The best gene annotation result was chosen by the two following principles: 1). the annotation with a clear functional description was firstly chosen; 2). the annotation with the best blast result (considering alignment coverage and identity) was chosen.
