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Collapse WU-BLAST
WU-BLAST basic Local Alignment Search Tool. Find regions of sequence similarity by querying your sequence against nucleotide and protein databases...
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Collapse ScanPS
ScanPS (Scan Protein Sequence) is a program for comparing a protein sequence to a database of protein sequences...
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Collapse FASTA
Sequence similarity searching of your query sequence against nucleotide and protein databases using the FASTA programs...
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Collapse MPsrch
MPsrch is a biological protein sequence comparison tool that implements the true Smith and Waterman algorithm...
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Collapse Parasite-BLAST
Parasite-BLAST finds regions of sequence similarity by querying your sequence against nucleotide parasite databases...
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Collapse Proteome, Genome & WGS FASTA
Using the FASTA programs Sequence similarity searching of your query sequence against:
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EBIToolsSimilarity & Homology

Similarity & Homology

Here the user will be able to use various sequence database similarity search tools such as FASTA, BLAST, MPsrch and ScanPS. 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   More Information & Help Documentation Washington University (WU) BLAST2 for protein databases. (BLAST 2.0 with gaps)

BLAST2-WU Nucleotide   More Information & Help Documentation

Washington University (WU) BLAST2 for nucleotide databases. (BLAST 2.0 with gaps)
BLAST2-NCBI Protein   More Information & Help Documentation NCBI BLAST2 (BLASTALL) program for protein databases.
BLAST2-NCBI Nucleotide   More Information & Help Documentation NCBI BLAST2 (BLASTALL) program for nucleotide databases.
BLAST2-NCBI EVEC   More Information & Help Documentation European BLAST2 Vector Searches. Check your sequences for vector contamination.
PSI-BLAST   More Information & Help Documentation [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   More Information & Help Documentation [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   More Information & Help Documentation Pattern Hit Initiated BLAST (PHI-BLAST) treats two occurrence of the same pattern within the query sequence as two independent sequences.
FASTA Nucleotide   More Information & Help Documentation Sequence similarity searching against nucleotide databases using FASTA.
FASTA Protein   More Information & Help Documentation Sequence similarity searching against protein databases using FASTA.
FASTA-Proteome Server   More Information & Help Documentation Completed Proteomes FASTA server.
FASTA-Genome Server   More Information & Help Documentation Completed Genomes FASTA server.
FASTA-WGS Server   More Information & Help Documentation Whole genome shotgun (WGS) FASTA server.

Rigorous Protein Searches

Tool Description
MPsrch   More Information & Help Documentation Anedabio, formerly Edinburgh Biocomputing
Systems' very fast  implementation of the true Smith and Waterman algorithm.
ScanPS 2.3   More Information & Help Documentation Version 2.3 of ScanPS Fast implementation of the true Smith & Waterman algorithm for protein database searches.
SSEARCH   More Information & Help Documentation SSEARCH is a full implementation of the Smith-Waterman algorithm with well-validated statistical estimates.

Specialised DNA Searches

Tool Description
BLAST2-ASD More Information & Help Documentation ASD BLAST server.
BLAST2-Parasite   More Information & Help Documentation Parasite Genomes BLAST server.
FASTA-ASD   More Information & Help Documentation Protein sequence similarity searching against the ASD Database using FASTA.
FASTA-LGIC Protein Server   More Information & Help Documentation Protein sequence similarity searching against the Ligand Gated Ion Channel Database using FASTA.
FASTA-LGIC Nucleotide Server   More Information & Help Documentation Nucleotide sequence similarity searching against the Ligand Gated Ion Channel Database using FASTA.
FASTA-SNP Server   More Information & Help Documentation 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

Search the UniProt Protein Resource


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