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PomBase website v2
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motif search #1225

Closed ValWood closed 5 years ago

ValWood commented 5 years ago

when I search with RXXS I can only see some of the results. Do we need a cut-off or can it be removed.

Also (and if we can't report the full list) it might be nice to order things like this so that the proteins with the most motif hits are at the top of the list

mah11 commented 5 years ago

If we keep the cut-off for the initial result display (I'm neutral), there should be a link to see, or at least download, all the hits - it's valuable to get the actual hit sequences and their context, not just the gene list.

Could it also be jazzed up to support "sort on this column"? If it's feasible I could open a separate ticket ...

ValWood commented 5 years ago

OK this has "discuss". Kim do you need to discuss? I put next on this because we have a news item for the changes.

kimrutherford commented 5 years ago

when I search with RXXS I can only see some of the results

Only the first 100 matching genes are shown but you'll get all the genes if you click the link to the advanced search.

Do we need a cut-off or can it be removed.

I'd like to keep a cut off of some sort so that it's not too slow, RXXS matches a lot of places in a lot of genes so the table becomes quite large.

ValWood commented 5 years ago

The problem with this is that you only know that a protein matches with the truncated list.

You can't see how many matches, or their positions in the sequence

so how about Misoris suggestions. You see the truncated list, and then you can click "more" to see the rest ?

kimrutherford commented 5 years ago

You see the truncated list, and then you can click "more" to see the rest ?

Yep, we can do that. I'll work on that later in the week.

kimrutherford commented 5 years ago

Could it also be jazzed up to support "sort on this column"? If it's feasible I could open a separate ticket

Is it just Gene and Product you'd want to sort on?

ValWood commented 5 years ago

No, unfortunately :( it would be more complicated. If we had that option we would want to sort so that the proteins with the largest number of occurrences of a motif were at the top.

If this is too hard put this as future, as long as people can extend the default list that will do as a first pass.

ValWood commented 5 years ago

Hi Kim, what do you still need to know here?

I think usefully just the option to "see all hits" is all we need?

kimrutherford commented 5 years ago

I've added a link to get all the matches when not all are shown.

ValWood commented 5 years ago

Something has changed though. Now you only see one hit at a time? I think people need to see all hits in a particular protein together, even if they can't see them all at once. Does that make sense?

kimrutherford commented 5 years ago

What motif were you looking at? I just tried "XXXXXX" and got lots of hits.

ValWood commented 5 years ago

yep ignore me. I searched for a rare motif only present once per protein if present!