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Since potential scores for motif predictions can be improved by alignment of multiple genomes [ 21], this approach here was adopted to detect regulatory motifs.
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This graph was used to generate a draft consensus map set that was improved by alignment of single molecules and recalculation of the relative label positions.
These differences can be improved by correcting the alignment errors of the MAST.
This can be improved by optimizing the alignment algorithm to tolerate a higher rate of errors and especially more indels.
The local alignment algorithm currently used in a BLASTn search should be improved by substituting a global alignment algorithm, such as the one used in the Barcode of Life Data System (BOLD [21], that is more efficient at aligning sequences with significant length variation and therefore more successful at matching them within a known sequence database.
Alignment performance may further be improved by combining several cross-species pairwise network alignments.
The accuracy of the predictions can considerably be improved by thorough multi-species intron alignments, which are, however, difficult to generate automatically and reliably.
More radically, alignment might be improved by an iterative approach to table construction.
ClustalW2 [ 50] was used to identify the PWMs where the alignment could be improved by introducing gaps.
Trace alignment would be improved by employing markers throughout the region of interest, but there is potential co-migration of analytes with the APTS-tagged mobility marker sugars.
Such alignments can be improved by increasing the signal-to-noise ratio through exclusion of noisy sites.
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