Editing Sequence analysis (section)

== Sequence alignment ==
{{Main|Sequence_alignment#Pairwise_alignment}}
 {{Main|Multiple sequence alignment}}

[[File:WPP domain alignment.PNG|thumb|650px|center|Example multiple sequence alignment]]

There are millions of [[protein sequence|protein]] and [[nucleotide]] sequences known. These sequences fall into many groups of related sequences known as [[protein family|protein families]] or gene families.  Relationships between these sequences are usually discovered by aligning them together and assigning this alignment a score. There are two main types of sequence alignment. Pair-wise sequence alignment only compares two sequences at a time and multiple sequence alignment compares many sequences. Two important algorithms for aligning pairs of sequences are the [[Needleman-Wunsch algorithm]] and the [[Smith-Waterman algorithm]]. Popular tools for sequence alignment include: 
*Pair-wise alignment - [[BLAST (biotechnology)|BLAST]], [[Dot plot (bioinformatics)|Dot plots]] 
*Multiple alignment - [[Clustal|ClustalW]], [[ProbCons|PROBCONS]], [[MUSCLE (alignment software)|MUSCLE]], [[MAFFT]], and  [[T-Coffee]].
A common use for pairwise sequence alignment is to take a sequence of interest and compare it to all known sequences in a database to identify [[Homology (biology)|homologous sequences]]. In general, the matches in the database are ordered to show the most closely related sequences first, followed by sequences with diminishing similarity. These matches are usually reported with a measure of statistical significance such as an [[Expectation value]].