In bioinformatics, sequence analysis is the processing of DNA,
RNA or peptide sequences by a range of
analytical methods to understand its structure or function.
Methodologies used, include sequence assembly,
sequence alignment and searches against biological databases.
Sequence assembly means the reconstruction of
a DNA sequence by aligning and merging small DNA fragments.
These small DNA fragments are the results from sequencing machine.
Thus, the sequence assembly process involves comparing sequences,
finding overlapping fragment pairs,
merging as many fragment pairs as possible
and creating a consensus sequence from the merged fragments.
The challenges in sequence assembly programs are to allow potential sequence ambiguities,
and yet discriminate between repetitive regions,
gene family members or gene sharing the same motif.
Sequence alignment is a method of comparing
two or more sequences by looking for a series of
individual characters or character patterns found in the same order in the sequences.
There are two main types of sequence alignment,
pair-wise sequence alignment and multiple sequence alignment.
Pair-wise sequence alignment only compares two sequences at a time.
Whereas multiple sequence alignment compares many sequences.
In order to find similar regions of a sequence,
it is common to perform a search using a sequence analysis tool.
A popular and widely used tool is a program called BLAST,
Basic Local Alignment Search Tool.
BLAST is a pair-wise alignment tool and used to search for sequence similarity.
More specifically, it is an algorithm for comparing
primary biological sequence information such as the nucleotides of DNA sequences.
A BLAST search enables a researcher to compare
a query sequence with a library or database of sequences,
and identify library sequences that
resemble the query sequence above a certain threshold.
These analytical methods can aid precision medicine.
For example, by providing a better understanding of genes involved in rare diseases.
This in turn can lead to the development of targeted therapies.
To put sequence analysis in a medical context,
sequencing results from a human DNA sample can be
mapped to a widely used reference sequence.
This reference sequence is produced from the Human Genome Project.
The reference sequence shows the position of our genes, most of which are known.
Sequence analysis identifies the differences,
called variants, between your genome and the reference.
Most differences are harmless.
However, some differences could be causing a particular medical condition.
Genetic testing can be used to find changes that are associated with inherited disorders.
The results of a genetic test can confirm or rule out a suspected genetic condition,
or help determine a person's chance of developing or passing on a genetic disorder.
For example, genetic testing can be done for cystic fibrosis.
Cystic fibrosis is a genetic condition,
which usually affects people from birth and causes a range of symptoms.
The main symptoms affect the lungs and digestive system.
A genetic test for cystic fibrosis will look for
the most common changes in the cystic fibrosis gene.
If you have a family history of cystic fibrosis,
you can be tested to determine whether you are
a carrier of the defective gene that causes this condition.
Sequencing data is an important part of precision medicine,
as its analysis enables personalized treatment and prevention of disease.
Each individual will benefit from targeted therapies,
meaning that fewer people will suffer from
unnecessary side effects that may occur with ineffective therapies.
Precision medicine aims to provide
better prevention and treatment methods for each individual,
none of which would be possible without the individual's sequencing results.
Dr Areti ManatakiTeaching and Research Fellow
Dr Frances WongData Science MOOC Project Lead
