3. Editing alignments :
When a multiple sequence alignment is generated with any kind of automatic program, it needs to be edited manually or in an editing program before presenting or publishing the alignment. Multiple Align Show (http://bioinformatics.org/sms/index.html) and Jalview (http://www.jalview.org/) are two such multiple alignment editors. Multiple Align Show accepts a group of aligned sequences (in FASTA or GDE format) and formats the alignment to specifications. The number of residues per line, the font size and font style, and colors for different regions can be specified. It is also possible to set a consensus level, which specifies the fraction of residues that need to be identical or similar in a column of the alignment for highlighting to be added. Multiple Align Show is one of many such programs that can be used to enhance the output of sequence alignment programs.
4. Interpreting the result of multiple sequence alignment :
It is possible to identify important positions or motifs in a protein from multiple alignment, which are conserved even when aligning distantly related proteins. When a good alignment with too many conserved positions is found, a few distantly related sequences can be added one by one and the effect of these sequences on the overall alignment quality can be checked. The sequences that BLAST reported
as marginal hits when first scanned SWiSS-PROT for homologous sequences can be construed as distantly related sequences. Initially aligned conserved patterns, if they survive after aligning with distantly related sequences, may be true conserved patterns. Other pattern-identifying tools such as ScanProsite and MotifScan hyperlinked in ExPASy Proteomics Server Site (http://ca.expasy.org/) can be used to verify these conserved patterns, revealed by the multiple sequence alignment.
The data obtained from multiple sequence alignment can be used to carry out phylogenetic studies. The word phylogenetics is derived from the Greek words, phylon, which means tribe or race, and genetikos, which means birth. Phylogenetics, also known as phylogenetic systematics, studies evolutionary relatedness among various groups of organisms. Phylogenetics is a special kind of phylogeny that studies the origin and evolution of a set of organisms. Thus, phylogenetics deals with identifying and understanding the relationships between the many different kinds of life on earth. In the past, phylogenetic analysis was heavily based on morphological data. Well-resolved molecular trees based on
molecular data (nuclear DNA and derived protein data) have become an important tool in phylogenetic analysis. Molecular trees can serve as scaffolds for investigating evolutionary relationships. Multiple sequence alignment can be used to study group of related genes or proteins to infer phylogenetic (evolutionary) relationships between genes and to discover patterns that are shared among groups of functionally or structurally related sequence.
