All lepidopteran DNA sequence accessions that passed filter criteria were downloaded in FASTA format, imported into the MEGA 5.0 sequence alignment application, and a multiple sequence alignment was made using the ClustalW algorithm (default parameters: gap opening penalty, 15; gap extension penalty, 6.66; weight matrix IUB, and transition weight, 0.5) in the MEGA 5.0 alignment module.
The role of the Application Server is to link the GATU client to the database search and sequence alignment applications the program uses; for convenience and enhanced speed, these may be installed on a more powerful machine or on a cluster.
As such, the presented Hamming discriminator is uniquely suitable for real-time image processing and alignment applications.
The FASTA formatted mitochondrial genome sequences were imported into the MEGA 4.0 software package sequence alignment application [34] and a multiple sequence alignment was performed with the ClustalW algorithm using default parameters (gap opening penalty 15, gap extension penalty 6.66, weight matrix IUB, and transition weight of 0.5).
These methods were widely used in aerospace, unmanned aerial vehicle, precision manufacturing, and optical alignment applications [4 6].
The computational power of our accelerator is comparable to that of a PC cluster consisting of 16 Intel-Xeon 2.0 GHz Quad CPUs for large-scale database alignment applications (cmsearch) with multiple input sequences, but the power consumption is only about 10% of that of the cluster.
Mainly two types of datasets are required in sequence alignment applications.
The ClustalW alignment application was used with optimal settings to align the resulting sequences and the haplotype(s) in each plant present was determined by visual inspection of the alignments.
Sequences were imported into a local database in BioEdit, searched using with Lep1 as the query and alignment of exon 1, intron 1, and exon 2 using the MEGA 5.0 sequence alignment application was created as described previously.
To this purpose, TUIUIU was applied as a preprocessing step of a multiple alignment application, leading to an overall execution time (filter plus alignment) on average 63 and at best 530 times smaller than before (direct alignment) and also, in some cases, to a qualitative improvement of the alignment obtained.
Figure 1 A set of scrambled views composing the Dolphin object prior coarse alignment application.
