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Conserved signature inserts and deletions (CSIs) in protein sequences provide an important category of molecular markers for understanding phylogenetic relationships. [1] [2] CSIs, brought about by rare genetic changes, provide useful phylogenetic markers that are generally of defined size and they are flanked on both sides by conserved regions to ensure their reliability.
Residues that are conserved across all sequences are highlighted in grey. Below the protein sequences is a key denoting conserved sequence (*), conservative mutations (:), semi-conservative mutations (.), and non-conservative mutations ( ).
Residues that are conserved across all sequences are highlighted in grey. Below each site (i.e., position) of the protein sequence alignment is a key denoting conserved sites (*), sites with conservative replacements (:), sites with semi-conservative replacements (.), and sites with non-conservative replacements ( ).
Given these observations, researchers hypothesized that other classes of self-cleaving ribozymes would also associate with these genetic elements. Therefore, searches were conducted on the non-coding regions nearby to the associated genetic elements to find conserved RNA structures using a previously established method. [3]
A genetic marker is a gene or DNA sequence with a known location on a chromosome that can be used to identify individuals or species. It can be described as a variation (which may arise due to mutation or alteration in the genomic loci) that can be observed.
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A database storing the sequence alignments of the most conserved regions of protein families. These alignments are used to derive the BLOSUM matrices. Only the sequences with a percentage of identity lower than the threshold are used. By using the block, counting the pairs of amino acids in each column of the multiple alignment.
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