When quantifying expression for differential expression analysis, only the primary alignments for each read were counted by HTSeq.
The "pm" invocation added the option "--primary", which counted just the primary alignments for reads, including reads that mapped multiple times but ignoring alignments not reported as a primary alignment for a read.
We thank Gillian Gibb for the primary alignment of avian mitochondrial genomes and software-human interface assistance and Warwick Allan for help with analyses.
On-the-fly alignment was used with quality control samples manually selected as the peak list for primary alignment.
This allows the user to gain knowledge of repetitive mappings specifically for those sections of the query that comprise a primary alignment.
The primary read alignment is done by seed-anchoring and local alignment.
The reason is that current structure prediction algorithms rely on the primary sequence alignment of reference structures, and differences for amino acids in stereochemistry and polarity are not taken into account during model calculation.
If a primary alignment matches the optimal alignment found by SSEARCH, it is a 'match'match
Ideally, ss-rRNA sequence alignments would use the conserved secondary structure to guide the primary sequence alignment.
For example, the generation of new alignments for each sequence is both computational costly, and does not take advantage of available curated alignments that make use of ss-RNA secondary structure to guide the primary sequence alignment.
