Sequence Similarity Searching is a method of searching sequence databases by using alignment to a query sequence. By statistically assessing how well database and query sequences match one can infer homology and transfer information to the query sequence.

The tools can be launched with different form pre-sets using the links - these can be changed on the tool page as well.


FASTA More Information & Help Documentation

FASTA is another commonly used sequence similarity search tool which uses heuristics for fast local alignment searching.

Protein Nucleotide Genomes Whole Genome Shotgun

SSEARCH More Information & Help Documentation

SSEARCH is an optimal (as opposed to heuristics-based) local alignment search tool using the Smith-Waterman algorithm. Optimal searches guarantee you find the best alignment score for your given parameters.

Protein Nucleotide Genomes Whole Genome Shotgun

PSI-Search More Information & Help Documentation

PSI-Search combines the sensitivity of the Smith-Waterman search algorithm (SSEARCH) with the PSI-BLAST profile construction strategy to find distantly related protein sequences.


GGSEARCH More Information & Help Documentation

GGSEARCH performs optimal global-global alignment searches using the Needleman-Wunsch algorithm.

Protein Nucleotide

GLSEARCH More Information & Help Documentation

GLSEARCH performs an optimal sequence search using alignments that are global in the query but local in the database sequence. This can be useful when you want to match all of a short query sequence to part of a larger database sequence.

Protein Nucleotide

FASTM/S/F More Information & Help Documentation

These specialist programs allow searches of databases using a group of short peptides as the query.

Protein Nucleotide


NCBI BLAST More Information & Help Documentation

NCBI BLAST is the most commonly used sequence similarity search tool. It uses heuristics to perform fast local alignment searches.

Protein Nucleotide Vectors

PSI-BLAST More Information & Help Documentation

PSI-BLAST allows users to construct and perform a BLAST search with a custom, position-specific, scoring matrix which can help find distant evolutionary relationships. PHI-BLAST functionality is also available to restrict results using patterns.


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.