DNA Sequence Alignment

Sequence alignment describes the way of aligning DNA, RNA, or protein sequences to highlight or identify similarities between DNA sequences. Typically, gaps have to be inserted into sequences so that identical or similar nucleotides or amino acids are aligned in columns. Here is an example:

Sequence alignment is often used in several biomedical research fields, including phylogenetics, biogeography, and evolution research.

Here is an example of a phylogenetics experiment that includes DNA sequence alignments. Our researcher works for a museum of natural history, and wants to study the evolutionary relation between several animal species he studies. A typical approach would be:

• Isolate DNA from each of the species studied
• Generate DNA sequences for a gene region, an entire gene, or several genes
• Assemble the DNA sequences for each species into separate "contigs"
• Edit the sequence assembly results to remove any errors
• Align the contig sequences to each other using a multiple sequence alignment program
• Verify any observed differences by going back to the original DNA sequences
• Correct the placement of gaps in the aligned sequences, if necessary
• Export the sequence alignment for further analysis with phylogenetics software, for example to generate phylogenetic trees

This web site provides links to commonly used programs and web resources for DNA sequence alignments. Since hundreds of different programs and relevant web sites exist, the goal is not to provide lists, but rather to concentrate on the most commonly used and the most useful sequence alignment software.