Finding clones for identified genes

Clones corresponding to identified genes from Project Component 2 are made available to Project Component 3 as candidates for in situ image experiments. The following protocol is run once for new GenBank accession numbers used as Putative IDs as they are added to the identified genes database, i.e., it is not rerun regularly.

For the purposes of this description:

• A clone id is the number part of an "IMAGE:#" string found as part of the GenBank description.
• An IC# is the unique identifier from Project Component 3 for an experiment that produces a series of in situ images.
• An identified gene is a GenBank accession number in the Project Component 2 database that is associated with one or more cell lines.

Protocol

• Fetch entry for the new accession number from GenBank and extract the new sequence. BLAST the new sequence against the Project Component 2 identified genes database. If the new accession number matches an identified gene (using the synonym criteria of within 2% in length and >= 98% identity) and the identified gene already has clones associated with it and those clones were not inherited, then the new accession number inherits the clone list from the identified gene.

  This step is required so that when a new accession number is actually a new version of an existing accession number, it is associated with the same set of clone ids.

• If the previous step does not yield a match, then BLAST the new sequence against the mouse EST database and retain the top 50 hits. Of the 50, retain IMAGE clone hits that satisfy the identification criteria (>= 90% contiguous section of EST must match at >= 95% identity). For each of these hits whose GenBank entry contains an I.M.A.G.E. clone ID, search for that ID at Research Genetics (which actually use the CloneRanger web interface at Invitogen for searching their catalog). Up to ten clone hits that are also found in CloneRanger are associated with the new accession number in the Project Component 2 database.

  New GenBank accession numbers and their associated clones may be downloaded from the Advanced Download page at the Baygenomics web site.