We downloaded D. melanogaster and D. pseudoobscura CDS sequences from http://www.flybase.org and aligned orthologous genes with MACSE (Ranwez et al. 2011), which performs in-frame alignments of protein-coding sequences.
In order to evaluate how different alignment programs perform in sequencing reads with low quality ends, we use the four alignment algorithms to map S1 and S2 before and after trimming off the low quality bases using BRAT trim [ 18], respectively.
The results on IRMBASE 2 and DIRMBASE 1 now tell us how the alignment programs perform in cases when it is unknown if every motive occurs in every sequence thus providing a more realistic basis for assessing the alignment quality on locally related sequences compared to the situation in the old IRMBASE 1 where every motive always occurred in every sequence.
On the other hand, for those subject sequences of lengths larger than the threshold, all the threads in a block will perform the alignment in parallel for only one subject sequence.
Using this new subroutine for aligning alignments, we can then perform multiple alignment in RAF using a standard progressive strategy (Feng and Doolittle, 1987).
If a sufficient global alignment is not found for an aligned read's pair, BWA will perform local alignment in the genomic region near where the read's pair is predicted to occur.
Two of the methods, MAFFT and hmmalign, are exceptionally fast and perform an alignment in seconds (Table 1).
We then generated five reversals and five translocations of random segments in the genome with size 10,000 bp each to evaluate the capability of these tools to perform an alignment in the presence of rearrangements.
Alignment of each retrieved orthologous data among all strains under investigation was performed in AMAP (Protein multiple alignment by sequence annealing) [ 37] with 0.5 as the gap factor.
Contigs were exported and alignment performed in Clustal X 1.83 [ 68] with default parameters.
This high ICC was a result of the pre-processing image alignment performed in the Garrioch et al. study (Section 2.1) to ensure that the same patch of retina was imaged.
