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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.
A general objective function is optimized during the simulation, most generally the "sum of pairs" maximization function introduced in dynamic programming-based MSA methods. A technique for protein sequences has been implemented in the software program SAGA (Sequence Alignment by Genetic Algorithm) [ 37 ] and its equivalent in RNA is called RAGA.
A consensus logo is a simplified variation of a sequence logo that can be embedded in text format. Like a sequence logo, a consensus logo is created from a collection of aligned protein or DNA/RNA sequences and conveys information about the conservation of each position of a sequence motif or sequence alignment [1] [4].
Sequence alignment is also a part of genome assembly, where sequences are aligned to find overlap so that contigs (long stretches of sequence) can be formed. [39] Another use is SNP analysis, where sequences from different individuals are aligned to find single basepairs that are often different in a population. [40]
Conserved sequences with a known function, such as protein domains, can also be used to predict the function of a sequence. Databases of conserved protein domains such as Pfam and the Conserved Domain Database can be used to annotate functional domains in predicted protein coding genes.
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 ( ).
Ab Initio gene prediction is an intrinsic method based on gene content and signal detection. Because of the inherent expense and difficulty in obtaining extrinsic evidence for many genes, it is also necessary to resort to ab initio gene finding, in which the genomic DNA sequence alone is systematically searched for certain tell-tale signs of protein-coding genes.
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.