REI scores can range from 0 to 1, with 1 indicating perfect conservation and 0 indicating no conservation. A sequence with an REI score of 1 is completely identical to its orthologs, while a sequence with an REI score of 0 has no similarity to its orthologs.
REI scores are often used to identify functional regions of DNA, such as genes and regulatory elements. These regions are typically more conserved than non-functional regions, so they will have higher REI scores.
REI scores can also be used to study the evolution of DNA sequences. By comparing the REI scores of orthologs from different species, researchers can determine which regions of DNA have been conserved over time and which regions have diverged.
Here is a step-by-step guide on how to read an REI:
1. Identify the DNA sequence of interest. This could be a gene, a regulatory element, or any other region of DNA.
2. Find the orthologs of the sequence of interest. This can be done using a variety of methods, such as BLAST searches or phylogenetic analysis.
3. Align the sequence of interest with its orthologs. This can be done using a variety of software programs, such as ClustalW or MUSCLE.
4. Calculate the REI score for the sequence of interest. This can be done using a variety of methods, such as the GERP++ or phastCons programs.
5. Interpret the REI score. A high REI score indicates that the sequence is well-conserved, while a low REI score indicates that the sequence is not well-conserved.
REI is a powerful tool for studying the evolution of DNA sequences. It can be used to identify functional regions of DNA, study the evolution of DNA sequences, and much more.