Bioinformatics Sequence Alignment

Sequence Alignment

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Sequence Alignment

In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a result of functional, structural, or evolutionary relationships between the sequences. Aligned sequences of nucleotide or amino acid residues are typically represented as rows within a matrix. Gaps are inserted between the residues so that identical or similar characters are aligned in successive columns. 

Very short or very similar sequences can be aligned by hand. However, most interesting problems require the alignment of lengthy, highly variable or extremely certain sequences that cannot be aligned solely by human effort. Instead, human knowledge is applied in constructing algorithms to produce high-quality sequence alignments, and occasionally in adjusting the final results to show patterns that are difficult to represent algorithmically.

The alignment is done among two sequences, known sequence called reference/subject sequence and unknown sequence called query sequence.


Global Alignments 

It is a form of global optimization that “forces” the alignment to span the entire length of all query sequences. Global alignments, which attempt to align every residue in every sequence, are most useful when the sequences in the query set are similar and of roughly equal size.

Local Alignments

It identifies regions of similarity within long sequences that are often widely divergent overall. Local alignments are often preferable, but can be more difficult to calculate because of the additional challenge of identifying the regions of similarity. Local alignments are more useful for dissimilar sequences that are suspected to have regions of similarity or similar sequence motifs within their larger sequence context.

A variety of computational algorithms have been applied to the sequence alignment problem. These include slow but formally correct methods like dynamic programming. These also include efficient, heuristic algorithms or probabilistic methods designed for large-scale database search, that do not guarantee to find best matches.

Hybrid methods, known as semi-global or “glocal” (short for global-local) methods, search for the best possible partial alignment of the two sequences. This can be especially useful when the downstream part of one sequence overlaps with the upstream part of the other sequence. In this case, neither global nor local alignment is entirely appropriate: a global alignment would attempt to force the alignment to extend beyond the region of overlap, while a local alignment might not fully cover the region of overlap. Another case where semi-global alignment is useful is when one sequence is short and the other is very long. In that case, the short sequence should be globally (fully) aligned but only a local (partial) alignment is desired for the long sequence.

Pairwise sequence alignment methods are used to find the best-matching piecewise (local or global) alignments of two query sequences. Pairwise alignments can only be used between two sequences at a time, but they are efficient to calculate and are often used for methods that do not require extreme precision. The three primary methods of producing pairwise alignments are dot-matrix methods, dynamic programming, and word methods. 

Multiple sequence alignment is an extension of pairwise alignment to incorporate more than two sequences at a time. Multiple alignment methods try to align all of the sequences in a given query set. Multiple alignments are often used in identifying  conserved sequence regions across a group of sequences hypothesized to be evolutionarily related. Such conserved sequence motifs can be used in conjunction with structural and mechanistic information to locate the catalytic active sites of enzymes. Multiple sequence alignments are computationally difficult to produce and most formulations of the problem lead to NP-complete combinatorial optimization problems.

Alignments could be used to:

  • Quantify the phylogenetic distance between two sequences
  • Look for functional domains
  • Compare a mRNA with its genomic region
  • Identify polymorphisms and mutations between sequences
  • Evolutionary prediction
  • Structural and functional prediction


  • Gapped BLAST

Alignments are conventionally shown as traces. In a symbolic sequence each base or residue monomer in each sequence is represented by a letter. The convention is to print the single-letter codes for the constituent monomers in order in a fixed font. 

Every element in a trace is either a match or a gap. Where a residue in one of two aligned sequences is identical to its counterpart in the other the corresponding amino-acid letter codes in the two sequences are vertically aligned in the trace, a match. When a residue in one sequence seems to have been deleted since the assumed divergence of the sequence from its counterpart, its “absence” is labelled by a dash in the derived sequence. Since these dashes represent “gaps” in one or other sequence, the action of inserting such spacers is known as gapping.

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