Can we do multiple DNA sequence alignment using the Needleman– Wunsch algorithm?

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Anil Tomar

Hi Harindra

Needleman-Wunch algorithm is used for global alignment...in which case the length of sequences should be equal, e.g. it is generally performed to compare two sequences of equal length.....

For aligning two sequences we do local alignment which utilizes Smith-Waterman algorithm....this algorith is utilized for databse searches by various tools SW Search, Fasta and Blast.

MSA is done by dynamic programming and for scoring, similar alignment strategies are applied depending on the needs.

regards

Harindra Sathkumara

Thanks everyone.

I'm not a bioinformatic person. I read this paper recently where it said:

Alignments were performed using the ClustalW algorithm within the Macvector software (version 12.0.3; Accelrys) or for trees, the Needleman– Wunsch algorithm (implemented within the R programming package) with matches scoring one and gaps and mismatches scoring zero to minimize Levenshtein distance between sequences and consensus.

All I need is to align the sequences (clustal or needleman -whatever they have used, apperantly) and build a phylogenetic tree. Please explain to me which algorith they have used for phylogenic construction?

Thanks

simply align your sequences by clustalW and you can construct a phylogenetic tree by clustalW too. If u wish u, can use a specific program for phylogenetic analysis, i.e. MEGA, Bosque, Phylip etc.

Pranav,

If they have used Clustalw, please tell me about the matrix, IUB or clustalw as well. Thanks

Rahul Arvind Jamdade

For alignment of sequences:

Preffer codon code aligner (download it here: http://www.codoncode.com/aligner/)

Use muscle algorithm there to align sequences (It is fastest method for multiple alignment)

Then export those sequences in MEGA 6 (download it here: http://www.megasoftware.net/mega.php)

Use ClustalW algorithm here to realign your sequences (Most accurate method)

Phylogenetic tree:

There are basically two types of phylogenetic methods, character based methods and distance based methods. Character-based methods based on discrete characters from molecular sequences from individual taxa.

On the other hand, distance-based methods is based on the distance, the degrees of differences between pairs of seqeuences.

Such distance will be used to construct the distance matrix between individual pairs of taxa.

There are two different algorithms in distance based methods.

The cluster-based and the optimality-based.

The cluster-based method algorithms build a phylogenetic tree based on a distance matrix starting from the most similar sequence pairs.

The algorithms of cluster-bsed include unweighted pair group method using arithmetic average (UPGMA) and neighbor joining (NJ).

If you want to assess tree reliability go for bootstrapping method during constructing of phylogenetic tree.

(Free software for phylogenetic tree : MEGA 6 (http://www.megasoftware.net/mega.php))

Instructions: both UPGMA and NJ methods are available in this software, use bootstrap (500 or more) to get reliability.

Hi Rahul,

Thanks for your response. At the same are you aware of a method to use Needleman-Wunnsch for multiple sequence alignments? Please keep me posted.

The Needleman-Wunsch algorithm works in the same way regardless of the length or complexity of sequences, and guarantees to find the best alignment. The Needleman-Wunsch algorithm is appropriate for finding the best alignment of two sequences which are (i) of the similar length; (ii) similar across their entire lengths. (If you want to find more, reffer: http://www.science.marshall.edu/murraye/Clearer%20Matrix%20slide%20show.pdf).