Both the forward and backward strand of the alignments were screened separately.
This probability can be computed using the forward and backward algorithms and the resulting alignment probability provides us with a measure of confidence about the (biological) relevance between the given symbols (i.e., nucleotides, amino acids).
Depending on whether the mapped read is located at the forward or backward strand we have to span the alignment window upstream or downstream.
The two degenerate backward primers were designed based on an alignment of the publicly available Tas1r1 sequences from human, mouse, dog, cat, and fox.
To account for fragment sizing error, TWIN modifies the FM-Index backward search algorithm to backtrack along possible alignment choices that are consistent with the current fragment in the query.
The two center pods are the only ones in the traditional side-by-side alignment, except that they both face backward.
The FM-index of alignment supports the LF-mapping and backward search, the key functionalities of the FM-index, but the LF-mapping and backward search of our index is significantly more involved than the original FM-index.
We used a backward stepwise feature selection method that utilizes the alignment to the HMM profiles based on recursive feature elimination (RFE) algorithm, termed HMM RFE (Guyon et al., 2002).
The resulting alignments are smooth everywhere and can have backward bends (i.e., "backtracking") to better fit terrain and land-use patterns.
The new suffix array of alignment enables us to support the LF-mapping and backward search, the key functionalities of the FM-index, regardless of gap existence in the alignment.
This alignment may be due, in part, to the explicit training on backward design in the presemester orientation and feedback on their assessment development.
