Ms. Aldana worked over short motifs, using the full range of her instrument, articulating long and fast lines.
Additionally, our approach allows estimation of the relative abundance of pseudoknot and other (e.g. tree) motifs using the "edge-cut" property of RNA graphs.
All non-redundant trimmed sequences were screened for repeat motifs using the Repeatmasker (http://www.repeatmasker.org/), SSRIT (Simple Sequence Repeat Identification) http://www.gramene.org/db/markers/ssrtool using Perl regular expressions to find perfect SSR within the sequences (Temnykh et al. 2001).
We here use k-mer word scores to visualize trends among sets of motifs, as well as to calculate inter-motif distances for clustering motifs using the HOPACH algorithm [53].
An analysis of the consensus family motifs using the PATCH program in the Transfac database indicated that 19 of the 30 consensus motifs contain sequences that correspond to experimentally confirmed binding sites for specific plant TFs (Table 1).
The putative 5′ regulatory sequences for the 12 OsGLP genes and the OsGLP8-6 insequencesequence (858 bp, only present in the indica sequence) were analyzed as a training set (N = 13) for statistically overrepresented sequence motifs using the MEME algorithm (Bailey et al. 2006; ESM Table 1; motif size = 2 11 bp, 15 motifs, +/− strand, p < 0.001).
gambiae (AgamP3.4) were scanned for microsatellite motifs using the SciRoKo3.4 software program [33].
We assessed the tendency for orthologous upstream regions to share motifs using the Jaccard index as an overlap score.
The discovered motifs were compared against two existing databases of known motifs using the STAMP tool [30].
We began by searching all VACV proteins for any potential sliding clamp motifs using the InterProScan program [14], [15] via the JIPS interface [16].
Amino acid sequences corresponding to all predicted CDS were screened against the curated Pfam-A profiles [80] for functional motifs using the perl script Pfam_scan.pl (Wellcome Trust Sanger Institute, UK) using default settings.
