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Isoform-level alignment is also improved by alignment to CAST.
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.
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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In comparison, only 10,533 reads improve by alignment to NCBIM37 (Table 2, entries in boldface type) of which only 3% (326 of 10,533 reads) improve by two or more categories (Table 2, entries in underlined boldface type).
A total of 458,297 reads improve by alignment to the CAST transcriptome (Table 2, italic entries), of which 93% (427,016 of 458,297 reads) improve by two or more categories (Table 2, underlined italic entries).
A total of 186,248 reads improve by alignment to the DO transcriptome (Table 2, italic entries) and most (146,083) improve by two or more categories (Table 2, underlined italic entries).
In comparison, only 5384 reads improve by alignment to NCBIM37 (Table 2, entries in boldface type) and only 77 improve by two or more categories (Table 2, entries in underlined boldface type).
On average, in the 10 25% sequence identity range, alignments are improved by 28 correctly aligned residues compared with alignments made using FUGUE's default substitution tables.
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.
As expected, the alignment accuracy in CpG island simulation data is substantially improved by suppressing multiple alignments (Table 10A, B).
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