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Other laboratory protocols can be implemented to sequence directly from a clinical sample with low nucleic acid concentration, including random PCR as well as multiple displacement amplification (MDA).
The iterative mapping strategy used in primates has not been implemented to sequence other Y chromosomes due to the cost associated with the technique.
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Finally, 'galign' is currently implemented to detect sequence reads containing only zero or one mismatch.
In this software, a strategy to drop-down origins and positions of chromosomal segments rather than every allele state is implemented to simulate sequence data and to accommodate complicated pedigree structures across multiple generations.
In the third homologous searching procedure, BLAST searches against the GenBank non-redundant protein database (nr) were implemented to extract sequences from an even larger spectrum of species.
In an attempt to populate GenDiS, the MQ approach was implemented to search in sequence databases starting from the entire 1961 PASS2 superfamilies.
The SHRiMP2 aligner was chosen as it has been tested and optimized specifically for mapping miRNA sequences using special parameters provided by the authors and can be implemented to align longer sequences with high sensitivity.
A simple genetic algorithm [38] was implemented to create peptide sequences.
Two methods are implemented to reconstruct ancestral sequences.
More work is being implemented to obtain longer sequences to confirm and extend these genotypic comparisons.
These four criteria were implemented to eliminate contaminant sequences and to ensure that only high quality reads were used in subsequent assemblies.
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