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To reduce biases due to this over-representation, one member of any pair of domain sequences that share more than 60% identity is discarded.
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The distance travelled in each individual segment was tested against the reference value in the database for the station-to-station identity assigned to it in the previous stage, and the classification identity was discarded if the mismatch between the values was greater than a certain threshold.
Alignments where the coverage was <0.96 of the length of the mRNA or EST and <98% sequence identity were discarded.
PDZ domain pairs with less than 50% sequence identity were discarded to reduce noise [ 34].
Putative alleles (>95% AA identity) were discarded, leaving 10 candidate distinct genes.
Reads mapping more than five places with this maximal identity were discarded from further analysis.
Transcript alignments with less than 90% EST length coverage or less than 95% alignment identity were discarded.
Loci with > 95% nucleotide identity were discarded to avoid false positives caused by phylogenetic trees with insufficient resolution.
TEs belonging to each family were aligned using the Mega 4 program [ 59], and sequence pairs with less than 80% identity were discarded.
mORFs aligning with ≥ 99% identity were discarded, and uORFs of all remaining pairs were aligned using needle and validated as above.
Where segment identities were discarded, the identity was set to '(unknown)' in the index, which may refer to either the algorithm failing to find an identity, or a move to/from/within the depot, while the train was not in service.
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