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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

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 More Information & Help Documentation (EMBOSS)

EMBOSS Needle creates an optimal global alignment of two sequences using the Needleman-Wunsch algorithm.

Protein Nucleotide

Stretcher More Information & Help Documentation (EMBOSS)

EMBOSS Stretcher uses a modification of the Needleman-Wunsch algorithm that allows larger sequences to be globally aligned.

Protein Nucleotide

Local Alignment

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 More Information & Help Documentation (EMBOSS)

EMBOSS Water uses the Smith-Waterman algorithm (modified for speed enhancements) to calculate the local alignment of two sequences.

Protein Nucleotide

Matcher More Information & Help Documentation (EMBOSS)

EMBOSS Matcher identifies local similarities between two sequences using a rigorous algorithm based on the LALIGN application.

Protein Nucleotide

LALIGN More Information & Help Documentation

LALIGN finds internal duplications by calculating non-intersecting local alignments of protein or DNA sequences.

Protein Nucleotide

Genomic Alignment

Genomic alignment tools concentrate on DNA (or to DNA) alignments while accounting for characteristics present in genomic data.

Wise2DBA More Information & Help Documentation

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.

Launch Wise2DBA

GeneWise More Information & Help Documentation

GeneWise compares a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors.

Launch GeneWise

PromoterWise More Information & Help Documentation

PromoterWise compares two DNA sequences allowing for inversions and translocations, ideal for promoters.

Launch PromoterWise

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.