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Table of Contents
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Tools
Converting Uppercase to Exons
Some genome browser tools such as the UCSC Genome Browser allow you to download a genomic sequence and specify introns as lowercase. pLOT can use this to automate annotating of exons from sequences formatted in this manner. See the example using NRF1.
DNA Element Search
pLOT has a number of tools for searching potential sequences of interest. Under the Tools menu, clicking the “DNA Elements Search Tool” menu (or pressing Ctrl+Alt+P) opens the Search window.
This windows allows for searching and annotating of potential:
- Bacterial promoter cores (sigma70)
- Shine-Dalgarno (bacterial ribosome binding) sequences
- Kozak signal
- Intron splice donor/acceptor (GT/AG and GC/AG)
- CAP binding sites
- Mef2 binding sites
The cutoff dropdown box can be used to set the stringency higher being more stringent and lower being less.
Converting Base Pair position to codon number
Converting codon number to Base Pair position
Converting an amino acid sequence to a DNA sequence
