finding deficiencies in WormMart

Model Organism: Worms WormBase
1

I am unable to find a list of deficiencies with corresponding genetic map positions for a given chromosome using WormMart. I’m looking for large (multiple-map-unit) “Df” deficiencies, not the small ok and tm knockout alleles. Is there any way to find this information without manually plowing through the genetic map window on Wormbase?

Thanks!

2

Maybe you tried this and found it unsatisfactory but it does give a partial list of Df…

go to Filters. click on the Molecular Details tab. select “molecular mutation type: deletion”. select “[Molecular] Affected Gene Count >=” and set it to 5. This yields deficiencies as large as 195kb.Iit appears wormmart doesn’t access “rearrangements”. Alternatively, you can browse rearrangements (Dfs, Dps, Inversions) by chromosome and import them into a spreadsheet to sort them yourself. (example: http://www.wormbase.org/db/gene/rearrange?name=III)

also here’s Robert Herman’s 1984 paper where he lists the mnDfs: http://www.genetics.org/cgi/reprint/108/2/331

i hope this helps

3

If you don’t want to make a spreadsheet for yourself, the Genetic Map books that the CGC used to put out have a tabular list of genomic rearrangements (Df’s and Dp’s) that you might find useful. A PDF of the 2003 map book can be found at this link.

4

Thanks for the responses. The link to http://www.wormbase.org/db/gene/rearrange?name=III is just what I was looking for. I was able to easily copy and paste the information into a spreadsheet. I’m also going to download the last available genetic map book to make sure the Wormbase query found them all.