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Additionally, in a preliminary alignment to genome, overlapping reads were aggregated together into contiguous intervals.
A preliminary alignment of the proteins was used to identify sequence gaps that were removed prior to the determination of sequence divergence.
A preliminary alignment was performed with the 61 different complete APNs protein sequences in the database.
A preliminary alignment was constructed using the ClustalW multiple sequence alignment server (http://www.genome.jp/tools/clustalw/) [ 30].
This paper expands on Hapler [ 12], a tool for assembling reliable haplotypes given a preliminary alignment of genetically diverse reads.
A preliminary alignment with several Silene taxa (GenBank accessions in Table 1 and 10 unpublished sequences with similar sequence diversity as the sequences used in the analyses) was used to get the initial primer sequences.
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The algorithms include a high-performance preliminary alignment, a compartment identification based on a formally defined model of adjacent duplicated regions, and a refined sequence alignment.
Preliminary alignment with an accuracy of about 80 μrad has been performed with laser alignment system and OTR screens used at the TTF accelerator for electron beam diagnostics.
A preliminary sequence alignment was performed in Geneious using a plugin for Muscle [31] followed by manual adjustments resulting in an unequivocal alignment.
A preliminary "SuperViterbi" alignment resulted (Fig S7).
The implementation calls for a preliminary spatial alignment using intrinsic anatomical landmarks.
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