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Most of the missing sequences in the sequenced genomes were in the telomeric regions or low sequence complexity areas of the eight chromosomes of C. parvum, and generally occurred in the two 454-sequenced and the published C. hominis genomes.
However, MP-EST may poorly perform in the presence of missing sequences in some genes.
Promoter regions with missing sequences in the alignment were treated as gaps and excluded.
Only a partial sequence was identified for CD8α due to missing sequences in the genome.
Alignment between the Sanger and 454 sequences revealed missing sequences in each of the assemblies.
Some segments could not be aligned in all four species, primarily because they represent new sequences recently inserted into the Fg genome, ancestral sequences deleted in one of the other species, or missing sequences in one of the draft genomes.
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At the end of "Different from the Others," we're told of a missing sequence in which a great hand descends over a German law book to cross out the entry for Paragraph 175.
Two of these EST sequences that have shown the lowest degree of missing sequence in our alignment have been included in the phylogenetic analysis.
Attempting to resolve the missing sequence in the SA1 genome surrounding the nad6 gene yielded an unexpected result.
We included only alignments where sequence from all four species was available; regions of ambiguity or missing sequence in the alignment, were treated as gaps.
However, missing sequence in three other DAB sequences (DAB-01bac, DAB-05bac, and DAB-09bac) was probably attributable to sequencing or assembly artifacts so these sequences may also represent functional genes.
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