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Overlapping alignments are similar to global alignments, i.e., alignments spanning from end to end for two maps of roughly equal length, but to search for overlap alignment gaps after the ends of either map are not penalized.
The resulting alignment spans 2045 characters.
The exonerate alignments spanning for at least the 70% of the pig queries were retained.
In fact, all 4 cases where REV-1 was found to be best, the sequences came from the Los Alamos National Laboratory HIV database subtype reference alignment spanning all common HIV-1 (clade M) subtypes.
We constructed the tree from a gapless region of the NA alignment spanning the entire ThiF domain except for the last two bases.
The corresponding super-alignment spans 41,292 amino acid positions and has 50.4% data coverage.
Second, specific and degenerate polymerase chain reaction (PCR) primers, able to amplify the intergenic sequence (IGS) between any combination of α- and β-tubulin genes in tandem were designed from sequence alignments spanning the entire Kinetoplastida.
To display alignments spanning multiple chromosomes (or on bacterial genomes spanning several plasmids), we envision two strategies.
The final alignments, spanning 12,648 nucleotide respectively 2,729 amino acid positions, were attained by concatenating all processed alignments.
In this way alignments spanning short repeats were not penalized, but alignments largely composed of likely repeats were removed.
The project spans from January 2012 to December 2014.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com