<P> The Burrows--Wheeler transform has been successfully applied to fast short read alignment in popular tools such as Bowtie and BWA . See FM - index . </P> <P> Structural alignments, which are usually specific to protein and sometimes RNA sequences, use information about the secondary and tertiary structure of the protein or RNA molecule to aid in aligning the sequences . These methods can be used for two or more sequences and typically produce local alignments; however, because they depend on the availability of structural information, they can only be used for sequences whose corresponding structures are known (usually through X-ray crystallography or NMR spectroscopy). Because both protein and RNA structure is more evolutionarily conserved than sequence, structural alignments can be more reliable between sequences that are very distantly related and that have diverged so extensively that sequence comparison cannot reliably detect their similarity . </P> <P> Structural alignments are used as the "gold standard" in evaluating alignments for homology - based protein structure prediction because they explicitly align regions of the protein sequence that are structurally similar rather than relying exclusively on sequence information . However, clearly structural alignments cannot be used in structure prediction because at least one sequence in the query set is the target to be modeled, for which the structure is not known . It has been shown that, given the structural alignment between a target and a template sequence, highly accurate models of the target protein sequence can be produced; a major stumbling block in homology - based structure prediction is the production of structurally accurate alignments given only sequence information . </P> <P> The DALI method, or distance matrix alignment, is a fragment - based method for constructing structural alignments based on contact similarity patterns between successive hexapeptides in the query sequences . It can generate pairwise or multiple alignments and identify a query sequence's structural neighbors in the Protein Data Bank (PDB). It has been used to construct the FSSP structural alignment database (Fold classification based on Structure - Structure alignment of Proteins, or Families of Structurally Similar Proteins). A DALI webserver can be accessed at DALI and the FSSP is located at The Dali Database . </P>

Which of the following determines the default alignment of each field