Similarity & Homology

Here the user will be able to use various sequence database similarity search tools such as FASTA, BLAST. Interactive as well as email submissions are available for each of these services.

The results of similarity searches can be valuable in inferring homology, see 2can pages. The following are links to the similarity search tools we have available at the EBI.

General DNA and Protein Searches

Tool	Description
BLAST2-WU Protein	Washington University (WU) BLAST2 for protein databases. (BLAST 2.0 with gaps)
BLAST2-WU Nucleotide	Washington University (WU) BLAST2 for nucleotide databases. (BLAST 2.0 with gaps)
BLAST2-NCBI Protein	NCBI BLAST2 (BLASTALL) program for protein databases.
BLAST2-NCBI Nucleotide	NCBI BLAST2 (BLASTALL) program for nucleotide databases.
BLAST2-NCBI EVEC	European BLAST2 Vector Searches. Check your sequences for vector contamination.
PSI-BLAST [New Version]	Position specific iterative BLAST (PSI-BLAST) refers to a feature of BLAST 2.0 in which a profile is automatically constructed from the first set of BLAST alignments.
PSI-BLAST [Old Version]	Position specific iterative BLAST (PSI-BLAST) refers to a feature of BLAST 2.0 in which a profile is automatically constructed from the first set of BLAST alignments.
PHI-BLAST	Pattern Hit Initiated BLAST (PHI-BLAST) treats two occurrence of the same pattern within the query sequence as two independent sequences.
FASTA Nucleotide	Sequence similarity searching against nucleotide databases using FASTA.
FASTA Protein	Sequence similarity searching against protein databases using FASTA.
FASTA-Proteome Server	Completed Proteomes FASTA server.
FASTA-Genome Server	Completed Genomes FASTA server.
FASTA-WGS Server	Whole genome shotgun (WGS) FASTA server.

Rigorous Protein Searches

Tool	Description
MPsrch	Anedabio, formerly Edinburgh Biocomputing Systems' very fast implementation of the true Smith and Waterman algorithm. Please Note This service will be retired on Dec. 30th 2009. For equivalent searches please use the SSEARCH or PSI-Search services.
ScanPS 2.3	Version 2.3 of ScanPS Fast implementation of the true Smith & Waterman algorithm for protein database searches. Please Note This service will be retired on Dec. 30th 2009. For equivalent searches please use the SSEARCH or PSI-Search services.
SSEARCH-Protein	SSEARCH is a full implementation of the Smith-Waterman algorithm with well-validated statistical estimates. Search against protein sequences.
SSEARCH-Proteomes NEW	SSEARCH is a full implementation of the Smith-Waterman algorithm with well-validated statistical estimates. Search against completed proteomes.
GGSEARCH	GGSEARCH compares a protein or DNA sequence to a sequence database producing global-global alignment (Needleman-Wunsch).
GLSEARCH	GLSEARCH compares a protein or DNA sequence to a sequence database.
PSI-Search	PSI-Search, similar to PSI-Blast, combines the Smith-Waterman search algorithm (SSEARCH) with the PSI-Blast (BLASTPGP) profile construction strategy to find distantly related protein sequences.

Please Note: The Blitz service is replaced by the SSEARCH and PSI-Search services.

Specialised DNA Searches

Tool	Description
BLAST2-ASD	ASD BLAST server.
BLAST2-Parasite	Parasite Genomes BLAST server.
FASTA-ASD	Protein sequence similarity searching against the ASD Database using FASTA.
FASTA-LGIC Protein Server	Protein sequence similarity searching against the Ligand Gated Ion Channel Database using FASTA.
FASTA-LGIC Nucleotide Server	Nucleotide sequence similarity searching against the Ligand Gated Ion Channel Database using FASTA.
FASTA-SNP Server	European SNP database (HGBASE) FASTA searches.

EMBL Tools

Other computational services at the EMBL (in Heidelberg) are available. These include tools for similarity searching, protein functional analysis and sequence analysis... more