Is it possible to search for a motif or ...

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Is it possible to search for a motif or pattern with BLAST?

There are two general approaches to this type of questions. First do you wish to find if motifs exist in your query sequence, or do you have a known motif and wish to find other protiens or nucleotides with this motif?

In the first case, finding motifs in your query sequence can be done for proteins using the CDD (Conserved Domain Database) and CDART (Conserved Domain Architecture Retrieval Tool) tools. CDD allows you to compare your protein to an database of alignments and profiles representing protein domains conserved in molecular evolution as well as 3-dimensional protein structures in the MMDB database. These tools use popular protien motif databases, PFam (http://pfam.wustl.edu/) and Smart (http://smart.embl-heidelberg.de) in addition to the MMDB database.

For conditions of the second case if you have a known motif and wish to identify other proteins with this motif you can use PHI-BLAST. PHI-BLAST searches take a motif pattern and protein sequence as input and then compares these to the NCBI protein databases looking for other proteins which contain conserved regions similar to the motif entered.

For nucleotides it is only possible to search with short query sequences representing your motif or region of interest with the Nucleotide BLAST "Search for short nearly exact matches" service from the main BLAST web page. This can find other sequences whicvh contain similar nucleotide patterns. however there are no database of nucleotide patterns which can identify patterns in your nucleotide query sequence.

You may also be interested in checking out other molecular biology web sites, such as those mentioned in the Other Molecular Biology Resources section at the end of this FAQ, for motif searching software.

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Other Frequently Asked Questions

• Q: Which BLAST program should I use?
• What is low-complexity sequence?
• Can I use BLAST to compare to two or more sequences in a multiple sequence alignment?
• Why do I get the message "ERROR: Blast: No valid letters to be indexed"?
• What are other Molecular Biology Resources?
• Why does my search timeout on the BLAST servers?
• How can I limit my search to a "subset" of database sequences?
• How can I search a batch of sequences with BLAST?
• How can I see low-similarity matches when there are many strong hits to my query sequence?
• Is it possible to search for a motif or pattern with BLAST?
• More...