Pairwise Sequence Alignment
Pairwise Sequence Alignment is used to identify regions of similarity that may indicate functional, structural and/or evolutionary relationships between two biological sequences (protein or nucleic acid).
By contrast, Multiple Sequence Alignment (MSA) is the alignment of three or more biological sequences of similar length. From the output of MSA applications, homology can be inferred and the evolutionary relationship between the sequences studied.
- Global Alignment
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Global alignment tools create an end-to-end alignment of the sequences to be aligned. There are separate forms for protein or nucleotide sequences.
- Needle
(EMBOSS) - EMBOSS Needle creates an optimal global alignment of two sequences using the Needleman-Wunsch algorithm.
- Stretcher (EMBOSS)
- EMBOSS Stretcher uses a modification of the Needleman-Wunsch algorithm that allows larger sequences to be globally aligned.
- Needle
- Local Alignment
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Local alignment tools find one, or more, alignments describing the most similar region(s) within the sequences to be aligned. There are separate forms for protein or nucleotide sequences.
- Water (EMBOSS)
- EMBOSS Water uses the Smith-Waterman algorithm (modified for speed enhancements) to calculate the local alignment of two sequences.
- Matcher (EMBOSS)
- EMBOSS Matcher identifies local similarities between two sequences using a rigorous algorithm based on the LALIGN application.
- LALIGN
- LALIGN finds internal duplications by calculating non-intersecting local alignments of protein or DNA sequences.
- Water
The tools described on this page are provided using our new bioinformatics analysis tools framework. If you have any feedback or encounter any issues please let us know via EBI support.