Sequential Alignment

In Bio-data processing, the sequential alignment is a manner of laying out the components (Nucléotide S or amino-acid) of DNA, ARN, or primary protein sequences to identify the zones of agreement which translate similarities or dissimilarities of historical nature. The aligned sequences are traditionally represented like lines of a matrix. Holes are laid out so as to align the common characters on successive columns.

When two sequences in an alignment divide a common ancestor, the discordances are interpreted like points of change or places of insertion or délétion.

Representations

Alignments are usually represented either graphically or in format text. In the majority of the representations of sequential alignments, the sequences are written in lines, are laid out so that the common components appear in successive columns. In format text, the columns aligned contain identical or similar characters, indicated by a coherent system of symbols. An asterisk is used to show the identity between columns. Many programs use color to differentiate information. For the DNA or ARN, the use of color allows to differentiate nucleotides. For protein alignments, it makes it possible to indicate the properties of the amino-acids, which helps to conclude on the conservation from the role from a substituted amino-acid.

When several sequences are concerned, a last line is added to conclude a consensus.

Sequential alignments can be provided in a broad variety of formats of files, depend for example on the special program used: FASTA format, GenBank,… However, in the research laboratories, the specific use of technical tools can reduce the choice of format.

Local and total alignments

Total alignments are more often used when the concerned sequences are similar and of equal size. A general technique, called Algorithme of Needleman-Wunsch is based on the dynamic programming.

Local alignments are more often used when two dissimilar sequences are suspected of having similar reasons in spite of the environment. The Algorithme of Smith-Waterman is a method of local alignment general also based on the dynamic programming.

With sufficiently identical sequences, it there no difference in the results.

Hybrid methods, semi-local methods, prove to be useful when…

Alignment per pair

The methods of alignment per pairs are used to find the correspondences between two alignments of continuations but do not ask for an extreme detail.

Method of the matrices by point

Dynamic programming

Methods by words

Multiple sequential alignment

Dynamic programming

Progressive methods

Iterative methods

To find the reason

Techniques resulting from data processing

Structural alignment

DALI

SSAP

Combinative extension

Phylogenetic analysis

References

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