[[Image:RPLP0_90_ClustalW_aln.gif|right|thumb|300px|First 90 positions of a protein multiple sequence alignment of instances of the acidic ribosomal protein P0 (L10E) from several organisms. Generated with [[ClustalW]].]]
The multiple alignment problem consists of inferring all [[Homology (biology)|homologous]] characters among multiple biological sequences. The characters may consist of single [[Nucleotide|
In [[Bioinformatics]], multiple alignment can be used to study [[evolutionary]] relationships between sequences of [[proteins]] or [[genes]]. Since the changes between gene sequences due to evolution are incremental, genes with a common evolutionary origin (or their protein products) can be compared by aligning identical or similar [[residues]].
nucleotides]], [[Amino acid|amino acids]], genes, or any sequence segments that may share an evolutionary origin.
Multiple alignments may be used to study which sequences have been conserved over time. This is the starting point of [[Comparative genomics|comparative genomics]] and [[Molecular phylogeny| molecular phylogenetics]] studies.
A multiple sequence alignment is a graphical representation where several DNA or protein sequences are ''aligned'' on top of each other so that [[residues]] likely to play equivalent roles in the aligned sequences occupy the same column.
The alignment may then be used to study, which regions of genes have been conserved, and which are sensitive to [[mutation]], over the years. This is very useful in designing experiments to test and modify the function of specific proteins, to predict the function and [[protein structure|structure of proteins]], and to identify new members of protein families.
The production of a protein sequence alignment is also a necessary step for the study of the [[phylogeny]] of a protein family.
==Multiple sequence alignment programs and techniques==
