Protein domain finder software

Piwi or accession e. PF to see all data for that entry. You can also browse through the list of all Pfam families. Enter a clan identifier e. Kazal or accession e. CL to see information about that clan.

You can also browse through a list of clans. Enter a sequence identifier e. GI numbers should be in the form "". Enter the PDB identifier e. You can also use the keyword search box at the top of every page.

If you find Pfam useful, please consider citing the reference that describes this work:. You have hidden the blog posts section. You can restore it here. Comments or questions on the site? Send a mail to pfam-help ebi. Please note: this site relies heavily on the use of javascript. The form will accept both protein and DNA sequences. We make no attempt to generate meaningful open reading frames.

The matches from all six searches are combined in the result tables. We check all sequences before running a search. In order to avoid problems with the validation of your sequence, you should use only plain, unformatted text.

Below are some of the validation checks that we apply to sequences. If you have problems getting your sequence to upload, please check that it passes all of these tests. Note that although we do allow FASTA-style header lines on a sequence, some characters in header lines can still cause the sequence to be rejected.

If in doubt, please remove header lines before pasting in your sequence. You can see examples of sequences that will successfully pass all of the validation tests by clicking the Example buttons below the search form. The form supports several search options for protein sequences.

Note that these controls will be disabled if you paste in a DNA sequence and will be ignored by the server when it searches your DNA. The default threshold for the HMM search is an E-value of 1. Note that this is different to the default for protein searches. Search for keywords within the textual data in the Pfam database. You can perform the same search from anywhere within the Pfam site, using the keyword search box at the top right-hand side of every page.

Search for sequence architectures using the PfamAlyzer either as a Java application recommended for most users or as an applet run via Web Start.

You may be requested to add the Pfam website to the list of Java security exceptions. To run as an application Ensure Java is installed. Java can be downloaded here.

Download the application here Some browsers will launch the jar file automatically. If not, open a terminal or console, change directory to the Downloads directory and type "java -jar PfamAlyzerApp. To run as an applet Ensure Java is installed. Download the applet here Some browsers will launch the jar file automatically.

If not, open a terminal or console, change directory to the Downloads directory and type "javaws PfamAlyzer.

PfamAlyzer is designed to provide insight into the Pfam protein domain database. It integrates and extends many popular Pfam tools and provides means for the study of domain architecture evolution. PfamAlyzer is implemented as a Java Web Start application and can be run directly from the browser or from the desktop.

If using Linux you may prefer to use the OS package manager. The default security settings in many browsers makes it difficult to run web start applications directly from this page, but PfamAlyzer can also be downloaded as a jar file and run as a desktop application. On some systems MacOS you may need to accept a security warning in the system security setup. There are more details about how to run the PfamAlyzer here. In general, Java does not grant applets access to the local computer's resources.

PfamAlyzer enables the user to enter sequences by means of cut-and-paste. HOW TO. CDD is a protein annotation resource that consists of a collection of well-annotated multiple sequence alignment models for ancient domains and full-length proteins. How To. The results of CD-Search are presented as an annotation of protein domains on the user query sequence illustrated example , and can be visualized as domain multiple sequence alignments with embedded user queries.

High confidence associations between a query sequence and conserved domains are shown as specific hits. Batch CD-Search serves as both a web application and a script interface for a conserved domain search on multiple protein sequences , accepting up to 4, proteins in a single job. It enables you to view a graphical display of the concise or full search result for any individual protein from your input list, or to download the results for the complete set of proteins.

Batch CD-Search Help. With either approach, the corresponding SPARCLE record s will display the name and functional label of the architecture, supporting evidence, and links to other proteins with the same architecture.

Input protein sequence.