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We designed a query (query 9) that assessed how many consensus sequences were present in each ligand excluding the pairing of PxxP with RxxPxxP and PxxPx [KR] because these minimotifs are children of PxxP.
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> Many contig consensus sequences were sufficiently long to cover full or nearly full transcripts (Fig. 2).
It resulted in the loss of many well classified consensus sequences that were shorter than the misclassified sequences.
If so, it was then aligned with as many of the consensus sequences as necessary to determine the number of recognisable repeats.
Further inspecting the reads mapping to the Aacp114k gene, we observed many differences between the consensus sequences not shared across individual samples (data not shown).
MYC protein is a transcription factor that activates expression of many genes through binding on consensus sequences.
Many of these annotations (47 consensus sequences) were validated through comparison with the CDD database using RPS-BLAST which compares a protein query sequence to a position-specific score matrix prepared from the underlying conserved protein domain alignment [ 43].
As a result, many of the resulting contigs were consensus sequences derived from an alignment of the two haplotypes.
Meanwhile, many motifs have been identified, and their consensus sequences are well known.
Projection projects all l-mers from the input sequences onto many buckets by hashing and then derives the consensus sequences to select some valid buckets.
Only for the PIL population of D. geniculata two specific consensus sequences were deduced due to too many ambiguous sites.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com