Help

1. The database offers a search (go to the "Search Collection" page) for gene names (e.g. LMNA), protein description (e.g. "synthetases"), image or published localization (e.g. "cytoplasm"), exon-tag insertion point (e.g. "intron 1").

2. Links to other database: Each entry in the Dynamic Proteomics is associated with a cDNA sequence, detailed annotation from the Ensembl (http://www.ensembl.org/) and Entrez (http://www.ncbi.nlm.nih.gov/Entrez/) databases. In additional, each protein has links to the GeneCards (http://www.genecards.org/), InterPro (http://www.ebi.ac.uk/interpro/) databases and UniProt (http://www.uniprot.org/) for protein sequence information.

3. On the "Search Dynamics" page, a user can search for one or more words in clones annotation (including the clone's Description, Function and Process) to get all entries that have available movies and dynamics. Click on "All Data" to see all available time-lapse fluorescence microscopy movies of proteins in the LARC library. For example, enter a word "apoptosis" in the "Function and Description" text box and click on "Search":

In the results table, a user get all entries in the LARC library connected to the "apoptosis" process (or have word "apoptosis" in the clone Description, Process or Function). At the next step, a user can align protein dynamics. Please, mark one or more check boxes for protein dynamics and click on "Generate graphs". The output presents protein dynamics for one or more proteins, and alignment of protein dynamics in nucleus, cytoplasm and total in case if two or more proteins are marked.

4. The "Sequence Analysis" page provides a powerful search engine for user sequences. Users can use up to 50 different DNA sequences and search over all cDNAs in the database. The query parameters are passed to the search engine using CGI. Query results are presented with a corresponding query or gene name. The results refer to the proteins in the Dynamic Proteomics database, links to their movies and dynamics. The alignment of proteins dynamics can be obtained from the result page.

The results contain a sequence-to-sequence comparison of sequences of interest to all full-length cDNA sequences of library clones. The information (annotation, movies and protein dynamics) appears on the output page.

5. DOWNLOAD IMAGES AND MOVIES DATA BY FTP.

To download all files on Linux please use

wget -r ftp://alon-serv.weizmann.ac.il/pub/dynamprot/

This will recursively download everything under dynamprot/ directory and build the entire same structure in your working directory.

For Windows please use some download manager of the ftp directory: ftp://alon-serv.weizmann.ac.il/pub/dynamprot/