Subsequently, the SMART [ 45] and Pfam [ 46] motif identification tools were used to identify predicted PP2C domains in all these candidate proteins.
A previous study [ 20] used ab initio motif-identification tools on 198 mouse OR promoters to show that motifs similar to O/E and homeodomain sites are enriched in OR promoters.
The unigene sequences (singlets and contigs) were then searched for the presence of SSR motifs using the MIcro SAtellite identification tool (MISA) available at.
For this we have designed a new tool, MotIV (Motif Identification and Validation), which is based on STAMP [21].
For enriched motif identification, ChIPseek integrates findMotifsGenome.pl, a tool from HOMER [ 18] which can identify enriched motifs in genomic regions, and use Weblogo and Ghostscript for sequence logo generation [ 35, 36].
SSR motifs were identified in 17 genomes using MISA (MIcroSAtellite identification tool) program downloaded from the Leibniz Institute of Plant Genetics and Crop Plant Research website (http://pgrc.ipk-gatersleben.de/misa/).
We utilized motif identification using conservation and relative abundance (MICRA), a motif discovery tool designed to analyze the low-resolution data produced using the DamID technique [ 25].
Thus, DNA sequences were searched for perfect microsatellites, with a basic motif of 2-8 bp, using the computer program MISA (MIcroSAtellite identification tool) [ 73].
In this study, 16 SSR markers, including nine di-, six tri-, and one hexa-nucleotide motifs were detected in the 17 identified BrGRFs using the online SSR identification tool SSRIT (Table 2).
The MIcro SAtellite identification tool (MISA) [ 33] was used to perform the search of 2 to 6 nucleotide motif repeats into the unigene dataset.
