Re: [Gmod-ajax] JBrowse substring name search

[Colin <col...@gm...>]

Hi there,
One option: make sprtn a separate field in the GFF. So maybe reformat the
GFF column 9 like this

ID=XB22065605;provisional=sprtn

Then use bin/generate-names.pl --nameAttributes id,provisional

Other option https://github.com/elsiklab/jbrowse_elasticsearch which does
true full text indexing but requires server side setup of elasticsearch

-Colin

On Mon, Aug 31, 2020 at 2:04 PM Vaneet Lotay <van...@uc...>
wrote:

> 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*
>
>
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