Sequence Similarity Searching

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 buttons - these can be changed on the tool page as well.

BLAST

NCBI BLAST

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

WU-BLAST

WU-BLAST is similar to NCBI BLAST but combines multiple parameter options into a simpler 'sensitivity' setting.

PSI-BLAST

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.

Protein

FASTA

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

SSEARCH

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.

PSI-Search

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.

Protein

GGSEARCH

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

GLSEARCH

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.

FASTM/S/F

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

ENA SEQUENCE SEARCH: The EBI has a new search tool which is far faster than BLAST, with only a marginal loss in search sensitivity.
Try it out at ENA Sequence Search.

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.