BLAST (Basic Local Alignment Search Tool)

BLASTN: Use this form to query a nucleotide sequence against a database of nucleotide sequences.

TBLASTN: Use this form to query an amino acid sequence against a database of translated nucleotide sequences.

TBLASTX: Use this form to query a translated nucleotide sequence against a database of translated nucleotide sequences.

BLASTP: Use this form to query an amino acid sequence against a database of protein sequences belonging to a single strain.

BLASTX: Use this form to query a translated nucleotide sequence against a database of protein sequences.

Important note on BLASTP and BLASTX searches:
It takes a very long time to run on the database of ALL protein sequences (>10 minutes per sequence). Please use DIAMOND (links below) for searching broader taxonomic groups or all protein sequences in the database.

DIAMOND BLASTP

The DIAMOND BLASTP command can be used as a fast and sensitive alternative to BLASTP searches. Using an amino acid query sequence, it can search a database of proteins sequences hundreds of times faster than BLASTP.

More details on DIAMOND are available at the developers' website or in the following publication:

Benjamin Buchfink, Chao Xie & Daniel H. Huson (2015).
Fast and Sensitive Protein Alignment using DIAMOND
Nature Methods, 12, 59–60 (2015) doi:10.1038/nmeth.3176.
PMID:25402007

On this site, you can use DIAMOND BLASTP to query an amino acid sequence against a protein sequence database. For searches of large data sets (e.g. protein sequences from ALL strains in this database), this is now the only available option.

DIAMOND BLASTX

The DIAMOND BLASTX command can be used as a fast and sensitive alternative to BLASTX searches. It translates a nucleotide sequence and performs and searches a database of protein sequences up to 20,000 times faster than the original BLASTX.

More details on DIAMOND are available at the developers' website

On this site, you can use DIAMOND BLASTX to translate a nucleotide sequence and query against a protein sequence database. For searches of large data sets (e.g. protein sequences from ALL strains in this database), this is now the only available option.

Search for DNA motifs

Go to DNA motif search form

Takes an IUPAC-formatted DNA motif and searches against genomic DNA sequences. Returns a list of genomic features containing that motif which can be applicable to finding putative transcription factor binding sites and other interesting motifs.

Retrieve Sequences

Go to sequence retrieval form

Enter sequence coordinates and strand for any replicon in this database and retrieve the DNA sequence and/or three-frame translation.