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All these motifs represent different instances of sequence conservation between promoters.
We decided to create a full knowledge base by populating the SO ontology with individual instances of sequence features.
Similarly, marsupials show another one of the few, clear instances of sequence heterochrony in mammals, with many cranial structures associated with feeding in the pouch also showing advanced development [ 5, 18, 19].
Typically this is done by attaching terms to an annotation in a separate format, such as a flat file or a database which describes instances of sequence data (Eilbeck and Lewis, 2004).
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Finally, we removed several instances of sequences where the reverse and forward strand differed in a frequent base substitution, and that base substitution was embedded in a characteristic 454 error.
However, there were several instances of sequences that group in a way contradictory to accepted classification.
For example, KE Salt Bridge (an instance of Structural Motif) contains β3-lysine (an instance of Sequence Motif).
It will be underestimated, however, if there is any instance of sequence homogenization at the monomeric level of the satellite DNA in the lineage.
We looked at a SNP rs6552934, having a read depth of 9 with 7 reads supporting G allele and 2 reads supporting A allele, that is called as GG in sequencing data but as heterozygous AG in bead chip; this instance of sequencing call clearly indicates that genotype calls using sequencing data can go wrong in regions of low coverage.
Searches using sequences of known orthology of our data set identified 26 instances of this sequence in the T. corallinus genome.
Since longer reads can only make the assembly process easier, these datasets still represent some of the hardest instances of the sequence assembly problem.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com