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For most clusters containing multiple consensus sequences or cluster singlets, a single Blast hit was selected for annotation.
For each consensus sequence, we have also reported the percent ambiguity in Figure 3 which is the percentage of each minimotif for which there are multiple consensus sequences.
Moreover, the white-to-black-coded Mosaic symbols remain compact, allowing multiple consensus sequences to be displayed in a tabular format.
Given that there were 10 different types of SH3 binding consensus minimotifs, we wanted to know to what extent did previously studied ligands have multiple consensus sequences.
Also, genome assembly usually is aimed at generating one consensus sequence, whereas in transcriptome assembly, alternative splicing can lead to multiple consensus sequences for one gene.
Consensus sequences were thus created from sequences having identical BLASTX hits in the three comparators, allowing multiple consensus sequences for a single HGG.
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Multiple consensus target sequences were generated for both seeds by first aligning the target sequences (VEGF-A and ICAM-1) relative to their shared seed sequences.
Some TFs have multiple known consensus sequences.
The average number of minimotif consensa per SH3 ligand was 2.3 indicating a tendency for each ligand sequence to have multiple SH3 consensus sequences.
Multiple IHF consensus sequences have been identified within the packaging initiation site (cos), and we here interrogate IHF– cos binding interactions using complementary electrophoretic mobility shift (EMS) and analytical ultracentrifugation (AUC) approaches.
For the analyses, we used a multiple alignment consensus sequence, which contains Gypsy LTR retrotransposon reverse transcriptase (RT) and partial integrase (Int) domains.
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