answer lies in genomes

Sequence  alignment
 ( click here for most freqeuntly used tools on sequece comparision )

It is the procedure of comparing two (pair wise ) or more (multiple ) sequences by searching for a series of  individual characters or character patterns that are in same order in the sequence.

Types-

1          Global alignment- here sequence which are of approximately of same length are  compared to match regions  globally

2          Local alignment -  here sequences are matched to find out locally similar region, conserved  domains etc

Methods

1. Dot matrix

2. Dynamic programming

Matrices used

• Nucleic acid PAM scoring matrices

 Tools for sequence alignment-

using Kwords method

• BLAST( web interface  and programme )

• FASTA( web interface and programme )

• LFASTA( web interface  and programme )

• other software packages   

(found in GCG commercial package whose equivalent free we based tools are found at sdsc workbench at http://workbench.sdsc.edu/  to use this an account has to be set up which is free and it provides you with a space on the web where you can work )

Local align-

• Bestfit

• lalign

Global-

• Gap

Dotmatrix

• dotter

Multiple sequence alignment

Global alignment-

• Clustalw or clustalx

• MSA

• PRALINE

ITERATIVE METHODS

• DIALIGN

• Multialign

• PRRP

• SAGA