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

Protein Nucleotide Genomes Whole Genome Shotgun


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



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

Protein Nucleotide


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


These specialist programs allow searches of databases using sequence fragments as the query.

Protein Nucleotide



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 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 search and sequence analysis tools APIs in 2019

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