[Gmod-ajax] JBrowse substring name search

[Vaneet L. <van...@uc...>]

Hello,

I was curious if in JBrowse when generating the name indexes for the genes, is there a way to make it possible to retrieve genes in the browser search by searching for a substring within the gene symbol, as opposed to always a prefix that starts from the beginning of the gene symbol?  The reason I ask is, for some of our Xenopus genes which are not annotated fully yet, we have a provisional gene format which consists of 2 pieces like this one for example:

XB22065605 [provisional:sprtn]

I could be mistaken, but it appears that in JBrowse you can search for many pieces of the gene symbol string, as long as you start from the 1st character, so in this example, begin typing 'XB....' to find it.  In this example it would be valuable for us to search for the provisional symbol in this string so 'sprtn' and find the result, but it doesn't work.  Is there any method we can use to generate those types of name indexes?  I know there's a -completionLimit parameter which retrieve more completions of the prefix for the gene symbol but I assume all those auto-completions still require the search term to begin with the first few characters of the string.

Thanks,

Vaneet

Vaneet Lotay
Xenbase Bioinformatician
716 ICT Building - University of Calgary
2500 University Drive NW
Calgary, AB T2N 1N4
CANADA