Briefly, mRNAs and ESTs were aligned to the genome using SIM4 [ 32] to obtain alignments with splice sites precisely defined.
First, all-vs-all BLASTp for all protein sequences of nine species was performed to obtain alignments with an E-value upper threshold of 10-5.
On a dataset like RV11, the improvement is much less marked (M-Coffee8 delivered alignments having an average accuracy of 37.5%) and one needs to restrict the combination to the four best non-template-based methods in order to obtain alignments with accuracy comparable to the best methods (Table 1).
Among the obtained alignments, those with TM-scores >0.6 for Fr-TM-align and those with Z-scores >2 for DaliLite were used as reference alignments, respectively.
We then adjusted the location and orientation of the initial fault models to obtain better alignment with the hypocenter distribution of their aftershocks in Figs. 2 and 3. We manually fit the data with our own eyes to estimate more robust and reliable fault geometry than that by fitting them with regression analysis because of the existence of events occurring off the main shock faults (Fig. 3).
Finally, for d = 15, we can obtain an alignment with a score slightly better than without the filter, while still being 14 times faster.
For d = 14, we can obtain an alignment with a score quite better than without the filter (406 rather than 263), with an overall execution that is 66 times faster.
Although the predominant size of the IPed RNA was 20 45 nt, we selected a longer RNA fraction (35 100 nt) to obtain unique alignment with the human genome after deep sequencing.
In each step of the iterative refinement process (Barton and Sternberg, 1987 ; Berger and Munson, 1991 ; Gotoh, 1993 ), an alignment is divided into two sub alignments and then the two sub alignments are realigned, according to the tree-dependent iterative strategy (Gotoh, 1996 ; Hirosawa et al., 1995 ), to obtain an alignment with a higher objective score.
The highest downstream false-positive rates were obtained after alignment with Bfast, followed by CLC Bio's Beta aligner, Nextgene, Mosaik, Stampy, and Bowtie 2. Novoalign and Smalt had the lowest downstream false-positive rates followed closely by Omixon and CLC.
