Although aligned start codons and identical length are not necessarily features of conserved sequences, this requirement provides us with a subset of the most reliable homologous ORFs; it also simplifies the alignments required for calculation of synonymous and non-synonymous mutation rates.
The alignments, requiring at least 90% pre-miRNA similarity and 100% mature miRNA similarity, were reserved for further study.
The longer conversion times for the shorter spacer are attributed to lower freedom of movement within the monolayer to achieve the spatial alignment required for the topochemical polymerization.
As the ITS2 regions contained many short repeats and gaps, the final alignment required some manual fine-scale modifications.
When CECs on vertically oriented NGs were exposed simultaneously to a horizontal EF, they aligned more robustly than to either cue alone and the enhanced alignment required rho signalling.
To determine the minimum level of read alignment required for reliable detection of transcripts, 80 highly expressed single-isoform genes with evenly distributed reads across the exons were inserted into a randomly generated test genome.
We generated the true INDEL call set by two steps: (1) used GATK UnifiedGenotyper to call INDELs from the BWA-MEM alignment, (2) performed manual inspection on the large INDELs from the Bowtie2 alignment (require at least 25% of the reads supporting an INDEL) [ 43].
The tree alignment requires us to align each state with at most one other state, but not two or more.
In addition, we searched for small insertions and deletions via gapped alignment of reads unmapped in the Maq alignment, requiring that candidate indel coordinates were sequenced as wildtype in the comparison strain.
The process of alignment requires the best overall match between the two sequences to be found first: this 'global alignment' is then followed by a finer-grained 'local alignment' that involves modifying the short sequences by, for example, inserting small gaps or deleting short stretches of the sequence.
