PAIRWISE SEQUENCE ALIGNMENT

Perform pairwise sequence alignments to determine the relatedness of a pair of sequences, align transcripts to genes, or find a gene within a genome, all within the same application you use for multiple sequence alignments and analysis.

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Use MegAlign Pro to easily perform multiple and pairwise sequence alignments.

Sometimes, examining a pair of sequences from a multiple sequence alignment directly may give you a better picture of the relatedness of the pair. Additionally, sometimes pairwise sequence alignment is simply more suitable than multiple alignment, for example, to align the sequence of an uncharacterized gene to the genome of a related reference strain. MegAlign Pro gives you the flexibility to perform local, global and semi-global pairwise sequence alignments using the industry standard Smith-Waterman and Needleman-Wunsch algorithms, all within the same application you use for multiple sequence alignments and post-alignment analysis. This makes it easy to further explore the relatedness of pairs of sequences from multiple alignments, align transcripts to genes, or find a gene within a genome.

Pairwise sequence alignment in 4 simple steps

Step 1

Add or select two sequences

Step 2

Select Align Pairwise

Step 3

Adjust parameters, or accept the defaults

Step 4

Analyze results!

Learn more about Pairwise Sequence Alignment

Resources | Tutorials | FAQs | Citations | User Guide

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Resources

Please see our resources below for more information on pairwise sequence alignment.

Simplifying Multiple Sequence Alignment and Analysis with MegAlign Pro Webinar

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Choosing the Best Alignment for Your Project

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Best Practices for Sequence Alignment in MegAlign Pro Webinar

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Answers to Your MegAlign Pro Webinar Questions

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Tutorials

Watch one of our videos or check out one of our written tutorials to learn more about using MegAlign Pro for pairwise sequence alignment.

Working with Tracks in MegAlign Pro

The tracks in MegAlign Pro allow you to view sequence details. In this video, learn how to specify which tracks to display, adjust track parameters, and control tracks from the overview and sequences views.

Merging and Realigning Sequences in MegAlign Pro

In this video, learn how to perform profile alignments to merge two alignments together. In addition, learn how to merge and realign additional sequences in your MegAlign Pro project.

Bookmarking Places in MegAlign Pro and GenVision Pro

This video describes how to use the Places panel in MegAlign Pro and GenVision Pro to bookmark locations of interest.

Adding Sequence Files for Alignment in MegAlign Pro

Learn how to load different nucleotide and protein sequences into MegAlign Pro for multiple and pairwise sequence alignment and phylogenetic trees. This video walks you through different ways to add and organize your sequence data prior to performing an alignment.

Supported File Types in MegAlign Pro

Learn about the different files types supported by MegAlign Pro, including FASTA files and GenBank files.

FAQs

When should I use a pairwise sequence alignment?

Use pairwise alignment when you are only interested in comparing two sequences. Additionally, there are situations where a multiple sequence alignment (MSA) might help identify pairs for sequences or sub-sequences that are worth a more detailed, pairwise comparison.

Which is better, multiple or pairwise alignment?

Both have different goals. If you want to see the evolutionary relatedness of a group of sequences by creating and viewing a phylogenetic tree, multiple sequence alignment is the best choice. Pairwise alignment is the ideal choice for comparing two sequences in detail.

What are the different pairwise alignment methods offered and how do I know which one to use?

MegAlign Pro features three pairwAise sequence alignment tools:

Local Pairwise Alignment is designed specifically to find the highest scoring aligned segments…

MegAlign Pro features three pairwAise sequence alignment tools:

Local Pairwise Alignment is designed specifically to find the highest scoring aligned segments of two sequences, even if the full extent of the two is not included in the final alignment.
Global Pairwise Alignment doesn’t try to find the best scoring segment, but instead requires that the full extent of both sequences be included in their results. There is no requirement or guarantee that the best scoring pair of aligned segments from a local alignment will be aligned in a global alignment.
Semi-Global Pairwise Alignment is a relatively new approach that is particularly suitable when the two sequences differ greatly in length. When that happens, the longer sequence will have overhangs on either end of the alignment. Since overhangs are represented with gaps, a global aligner will attempt to increase the match score and minimize accumulated gap penalties by aligning parts of the shorter sequence to overhanging sequence region(s). This effect can produce a number of unrealistic, usually small aligned segments spaced by gaps near the ends of the alignment. Semi-global alignment is designed to address this problem by not penalizing gaps in overhangs (aka “end gaps”).

How do I export an image of my pairwise sequence alignment?

File > Export Image > (View Name). to export an image of your alignment for publication as an Adobe PDF (.pdf), Microsoft PowerPoint-optimized (.pptx), PNG image (.png) or JPG image (.jpg, .jpeg) file.

Can I perform a pairwise alignment within my multiple sequence alignment?

Yes, it is sometimes helpful to run a pairwise alignment to resolve a confusing placement of gaps within a multiple alignment. To do this, select the two sequences of interest, right-click on either name and select Align Pairwise.

Citations

Complete genome analysis of echovirus 30 strains isolated from hand-foot-and-mouth disease in Yunnan province, China
Zhang, M., He, D., Liu, Y. et al (2023). Virol J 20, 215. https://doi.org/10.1186/s12985-023-02179-9.

Comparative evaluation of current biochemical-, sequencing-, and proteomic-based identification methods for the Streptococcus bovis group
Putnam NE, Youn J-H, Wallace MA et al. (2023). Journal of Clinical Microbiology, Vol. 61, No. 4. https://doi.org/10.1128/jcm.01712-22.

Continuous clinicopathological and molecular recognition of very virulent infectious bursal disease virus in commercial broiler chickens
Ahmed Setta, Nahed Yehia, Momtaz Shaheen, Ashwag Shami et al. (2023), Poultry Science, 2023, 103306, ISSN 0032-5791. https://doi.org/10.1016/j.psj.2023.103306.

Emerging novel coronavirus (2019-nCoV)—current scenario, evolutionary perspective based on genome analysis and recent developments
Yashpal Singh Malik, Shubhankar Sircar, Sudipta Bhat, Khan Sharun, Kuldeep Dhama, Maryam Dadar, Ruchi Tiwari & Wanpen Chaicumpa (2020). Veterinary Quarterly, 40:1, 68-76, https://doi.org/10.1080/01652176.2020.1727993.

Genetic characterization of a novel picornavirus in Algerian bats: co-evolution analysis of bat-related picornaviruses
Zeghbib, S., Herczeg, R., Kemenesi, G. et al. Sci Rep 9, 15706 (2019) https://doi.org/10.1038/s41598-019-52209-2.

Genome alterations associated with improved transformation efficiency in Lactobacillus reuteri
Ortiz-Velez, L., Ortiz-Villalobos, J., Schulman, A. et al. Microb Cell Fact 17, 138 (2018) https://doi.org/10.1186/s12934-018-0986-8.

Identification of Hsp90 inhibitors with anti-Plasmodium activity
Posfai D, Eubanks AL, Keim AI, Lu K-Y, Wang GZ, Hughes PF, Kato N, Haystead TA, Derbyshire ER. 2018. Antimicrob Agents Chemother 62:e01799-17. https://doi.org/10.1128/AAC.01799-17.

Phylogenetic and mutational analyses of human LEUTX, a homeobox gene implicated in embryogenesis
Katayama, S., Ranga, V., Jouhilahti, E. et al. (2018). Sci Rep 8, 17421. https://doi.org/10.1038/s41598-018-35547-5.

16SrII phytoplasma associated with date palm and Mexican fan palm in Saudi Arabia
Omar, A.F., Alsohim, A., Rehan, M.R. et al. Australasian Plant Dis. Notes (2018) 13: 39. https://doi.org/10.1007/s13314-018-0326-1.

Potato purple top disease associated with the novel subgroup 16SrII-X phytoplasma
Omar et al. (2018). Int J Syst Evol Microbiol 68:3678–3682. https://doi.org/10.1099/ijsem.0.00303.

Genetic relationship between neuropteran families (Insecta, Neuropterida, Neuroptera) based on cytochrome oxidase-i sequences
Mirmoayedi, Alinaghi & Khah, Fatemeh & Kahrizi, Danial & Yari, Kheirollah. (2018). Genetika. 50. 717-730. 10.2298/GENSR1802717M.

Molecular characterization and phylogenetic analysis of Trypanosoma evansi from Northern India based on 18S ribosomal gene
Rajender Kumar, S.P. Sarkhel, Saroj Kumar, Kanisht Batra, Khushboo Sethi, Shikha Jain, Sanjay Kumar, B.N. Tripathi. Veterinary Parasitology: Regional Studies and Reports, Volume 15,2019,100259,ISSN 2405-9390. https://doi.org/10.1016/j.vprsr.2018.100259.

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Intuitive and easy to use

“MegAlign Pro is very intuitive and easy to use. Results are instantaneous.”

Ines Santisteban, Duke University
Easy to use

“Graphical representations are easy to use and aid in understanding relationships.”

Mark Maffitt, Epicentre Biotechnologies
Comprehensive

“Most comprehensive and full-feature alignment software I have found.”

Gordon Wolfe, California State University Chico

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