PIMA profile search

Search a library of profiles with a protein sequence

Query submission form

    This tool allows you to search our library of functional diagnostic profiles with a protein sequence. A match to one or more of these profiles provides you with an effective multi-alignment of your query sequence to the best-matched profile's defining set of proteins along with its annotations (see example output). This in turn allows one to propose that the matching sequence contains a domain of similar structure and function. Note that many of these profiles are of sufficient length that they cover the entire domain rather than some small fraction.

    Although the current database of available profiles is growing rapidly, your sequence may not match any of them at a statistically significant level. If you desire a profile for your unmatched sequence, you may email in the sequence requesting a profile to be generated. We plan to implement this feature as a web page in the future.

    You may search the annotations for the current profiles for functional keywords to see what functional domains are represented. If a given profile matched a PDB sequence, that id has been included in the annotation as well as the keyword PDB.

    The sequence must be in fasta format, but may be filtered, such as by XNU. The substitution character for marked out residues must be an X. Please see our profile summary for more information on what our profiles represent and why.

    Be advised that this search takes quite a while to run. As with all of our tools, we do not save your query data, or the results of your search. Any temporary files that were necessary to create are deleted before you see a display. We therefore suggest that you save any data you may be interested in so as to avoid the delay of making the same query again later.

NOTICE: Our databases and tools are currently being updated and repared. While we are doing our best to not have any services interupted, but we are aware that there are some broken data links. We hope to have this process completed as soon as possible.

Profile request form:

Please enter your full email address below:

Paste your sequence into the box below - must be in FastA format: