Quick Links

Useful Resources

Sequence alignments

The alignment of biological sequences is probably one of the most important and most accomplished in the field of bioinformatics. The ultimate goal of sequence alignment is to determine the similarity between different sequences.

Applications

• Gene finding: Having identified all ORFs of a genome can be used their lengths to estimate the probability of actually constituting genes, these are ab initio methods mentioned before. On the other hand, if there is a gene from another organism with a good alignment with the ORF found, there is strong evidence that this ORF is a gene.
• Function prediction: The alignment of sequences to determine if two genes are similar. That way if the first function of these genes is known we can assign the same function as the second. Genome Sequence Assembly: the de-novo assembly is a very important task in bioinformatics is based on the alignments between short DNA sequences obtained by the new-generation sequencers.
• One of the main applications of sequence alignment is the identification of homologous genes. Living organisms share a large number of genes descended from common ancestors and have been maintained in different organisms due to its functionality but accumulate differences that have diverged from each other. These differences may be due to mutations that change a symbol (nucleotide or amino acid) for another or insertions / deletions, indels, which insert or delete a symbol in the corresponding sequence.

Two genes are homologous if they share a common ancestor. Therefore, the homology is a dichotomous characteristic, i.e., given two genes are either homologous genes or not. However, given two sequences corresponding to two genes, can be said that there are different levels of similarity based on an alignment between them. The key task is to determine whether a good alignment between two sequences is significant enough to consider that both genes are homologous.
There are two different forms of homology. When the origin of two homologous genes is due to a process of gene duplication within the same species these genes are called paralogs, whereas when the origin is due to a speciation process/ event resulting in homologous genes in these different species are called orthologs.

Pairwise sequence alignment

Pairwise alignments are comparison of two sequences. This can be done to determine evolutionary relationships, predict protein function and structure.
To view pairwise sequence alignment, the sequences can be viewed using a dotplot matrix, where two sequences are represented along the x- and y- axis, a dot placed at the grid where the two sequences have identical residues; as shown below:
Diagonals correspond to conserved regions. A score is calculated by awarding a "reward" (positive score) for matching residues, and a penalty (negative score) for mismatches (gaps and substitutions). For example:

KAWRTY | ||:| KGWRSY

If Match = 5; Mismatch = 0; the score for the example shown is 5+0+5+5+0+5 = 20

Conservative substitutions are when a residue is replaced by a residue with similar physiochemical properties. Therefore, substitutions that are conserved are less penalised from mismatches. eg Glutamate-Aspartate (Acidic amino acids) Serine-Threonine (-OH sidechain)
As a result, a matrix is prepared to give different scores of residues based on the likelihood of occurence in nature/ evolution.

Multiple sequence alignment

Multiple sequence alignments are as a result of aligning multiple sequences. They are used to:

• Identify conserved sequence regions- Conservation is indicative of functional importance
• Constructing of profiles- eg for further database searching
• Prefiction of structural features, eg alpha-helices, loops, etc.

Alignment software