The algorithm dynamically considers various candidate alignments, partitions each candidate alignment into sections, and determines the most appropriate set of parameter values for each section of the alignment.
The new method is based on creating flexible, efficient whole genome indexes to rapidly map reads to candidate alignment locations, with arbitrary multiple independent indexes allowed to achieve robustness against read errors and sequence variants.
First, using multiple indexes of the reference genome, BFAST identifies candidate alignment locations (CALs) for each read.
In addition, we design a stochastic parallel framework that significantly speeds up the simultaneous refinement of multiple alignment candidates.
Multiple sequence alignments of candidate transcripts and their respective homologs were generated using the E-INS-i algorithm in MAFFT v7.0 [ 52].
It is furthermore of interest to use the homology information from multiple structural alignments of ncRNA candidates for interaction prediction.
To assess the presence and conservation of motifs in candidate green plant tRNase Zs, we performed multiple sequence alignments of identified tRNase Zs sequences.
Candidate positions in addition to information available in Dindel50 were subsequently analysed where the local multiple sequence alignments were further refined and associated quality scores recomputed.
Motif candidates are selected from multiple alignments whereas pairwise local alignments are retained for evaluating lineage specific motif abundance, which we will not discuss here.
Following a multiple alignment of the candidate locus with the other orthologous loci using BioEdit [ 61] primer design was attempted in regions with sequence divergence between the different loci.
