dictyBase Help: dictyMart

dictyBase Help: dictyMart

[dictyMart HELP INDEX]

How do I get the protein sequence of all protein kinases?

  1. Select the Dataset : "Genes" (should be selected by default)

  2. Click "NEXT"

  3. Here you select the dataset more precisely. You can make use of the Gene Ontology term "protein amino acid phosphorylation" (GO:0006468), to which all kinases are annotated.
    Enter " GO:0006468" in the Gene Ontology box, making sure to click the checkbox next to it.

    NOTE: You could also use "protein kinase activity" (GO:0004672), "protein tyrosine kinase activity" (GO:0004713), or "protein serine/threonine kinase activity" (GO:0004674). Since these terms are more specific, only a subset of the protein kinases will be retrieved for each of these queries.

    GO terms can be found in by searching dictyBase from the Search box in the upper-right corner of every page, or using the Gene Ontology browser AmiGO.

  4. You should also select "Primary Features" in the "Transcript subtypes" (3rd box in the page) to make sure you only get one sequence per gene in the output (see step 8). If you don't select that you will get two sequences per gene if there is a gene prediction AND a curated model.

  5. Click "NEXT"

  6. You are now on the "Select the Attribute Page", which will let you select what information to display. In the pull-down menu right below " Select the Attribute Page", choose "Sequences". The page will now show you slightly different options.

  7. To download protein sequences, select "Peptide" in the type of sequence to export.

  8. For clarity you probably want to also select "dictyBase ID" and "Gene Name" under "Header information".

  9. Click on "EXPORT", and you have a FASTA formated list of protein sequences for the genes with GO annotation = "protein kinase".

dictyMart is an implementation of the Biomart Project. BioMart is a query-oriented data management system developed jointly by the European Bioinformatics Institute (EBI) and Cold Spring Harbor Laboratory (CSHL). Visit the BioMart website for additional documentation.

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