This leads to differences in the length of the homologous The relative positions of nucleotides within the same gene in different species and in duplicated genomic regions are disturbedīy insertion and deletion of stretches of DNA over evolutionary time. Because of the central role theseĪlignments now play in our endeavors to establish the tree of life and to identify important parts of genomes through evolutionaryįunctional genomics, we see a need for increased community effort to investigate influences of alignment bias on the accuracy
To be used somewhat like benign formatting operations to make sequences equal in length. However, our understanding of alignment biases remains rudimentary, and sequence alignment procedures continue Errors in sequence alignmentĪre also found to have a significant negative effect on subsequent inference of sequence divergence, phylogenetic trees, andĬonserved motifs. A survey of investigations into strengths and weaknesses of sequenceĪlignments reveals, as expected, that alignment quality is generally poor for two distantly related sequences and can oftenīe improved by adding additional sequences as stepping stones between distantly related species. To errors and biases inherent in all sequence alignments. On downstream analyses, it is important to know the extent to which the inferences drawn from these alignments are robust While it is mere common sense that inaccuracies in multiple sequence alignments can have detrimental effects Sequence motifs, estimation of evolutionary divergence between sequences, and inference of historical relationships among DNA sequence alignment is a prerequisite to virtually all comparative genomic analyses, including the identification of conserved
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