The five quality related statistics used were the percentage of clusters passed filtering (%PF clusters), mean quality score (PF clusters), percentage of reads aligned, mean alignment score and percentage of alignment error, and had the following population means and standard deviations, respectively, 93.39 ± 1.85, 36.34 ± 0.5, 72.24 ± 3.0, 290.6 ± 15.13 and 0.98 ± 0.15.
Overall for the numbered chromosomes (not including random, chrM or chrUn), 86.33% of zebra finch sites could be aligned (mean: 77.26 ± 17.69; see Table 2).From this alignment we also calculated the genetic distance between amakihi and zebra finch as 0.0905 (Kimura two parameter model; see Table 2).
All these hits are likely true homologs, because sequence identity was high (mean: 91.3%, range: 87.1%–97.4%), as was the proportion of known pre-miRNA sequence aligned (mean: 87.0%, range: 58.3%–98.5%), strongly supporting that the five novel mouse candidates are true pre-miRNAs.
A greater proportion of the poly(A) than the Ribo-Zero libraries tended to be aligned (mean difference 11%%, median 8%%).
The aligned mean insert size was 188.76 bp (standard deviation = 44.81 bp) for males and 167.62 bp (standard deviation = 37.29 bp) for females.
The initial state in this iterative routine corresponds to a rough alignment where micrographs are aligned by means of simple cross-correlations.
The device is composed of a positioning stage and a vacuum sample-holder, which can be aligned by means of two alignment screws.
The DNA-sequences were multiply aligned by means of the ClustalX v1.83 [ 37] and the alignments were manually refined using the GeneDoc v2.7 [ 38].
A set of predicted DtxR binding sites was aligned by means of the CLUSTAL X program [ 21], and the resulting alignment was used to create a HMM by using the HMMBUILD module.
Therefore, in order to overlap the input data well, the reference data is aligned by means of a particle filter.
