It then determines the possible location of gaps in the alignment based on splice junctions flanking the aligned reads and uses gapped alignments to align the reads that were not aligned by Bowtie in the first step.
The P-score is the negative logarithm of the p-value, which accounts for RMSD, number of aligned residues (Nalgn) and number of gaps in the alignment (Ngap).
However, this scoring method considers only the parts of the structures that align and does not take into account gaps in the alignment, which would account for potentially important deletions and insertions.
The pair wise-deletion option was used to treat gaps in the alignment of GPAT, LPAT or DGAT sequences.
Our previous SVD-based flexible fitting approach can only take into account positions with no gaps in the alignment, being appropriate when the superfamily members are relatively similar and there are few gaps.
Gaps in the alignment were not used in the reconstruction.
Because there could be gaps in the alignment of cDNA sequence and the human genome sequence, the nucleotide position was converted considering possible gaps in the alignment.
In particular, varying the amount of gaps in the alignment had an impact.
The best alignment could be the one with continuous helix or strand uninterrupted by gaps in the alignment.
The frequency of mismatches and gaps in the alignment between contig sequences and the reference genome was determined by BLAST.
Two scores were calculated for each alignment, based on inclusion or exclusion of gaps in the alignment.
