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 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.
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 finds internal duplications by calculating non-intersecting local alignments of protein or DNA sequences.
Genomic alignment tools concentrate on DNA (or to DNA) alignments while accounting for characteristics present in genomic data.
Wise2DBA (DNA Block Aligner) aligns two sequences under the assumption that the sequences share a number of colinear blocks of conservation separated by potentially large and varied lengths of DNA in the two sequences.
GeneWise compares a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors.
PromoterWise compares two DNA sequences allowing for inversions and translocations, ideal for promoters.
The tools described on this page are provided using the EMBL-EBI bioinformatics web and programmatic tools framework. If you have any feedback or encounter any issues please let us know via EMBL-EBI support.