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rkweku / miRador

Plant miRNA identification tool that utilizes a variety of filters to validate predicted miRNAs
GNU General Public License v3.0
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Can multiple species in the miRBase be selected as reference sequences #4

Open aijigekoukou-shen opened 3 years ago

aijigekoukou-shen commented 3 years ago

Hi

When I use miRador, it seems that I can only choose one species in miRBase as a reference，So I have a few questions.

1) Can multiple species or all plants in miRBase be selected as reference sequences?

2) Do we have to refer to the miRBase database? Why not try other better miRNA data, like the sRNAanno database (http://www.plantsrnas.org/)?

3) Can users provide reference miRNA sequences independently? As we all know, there is a big problem with the miRBase database.

4) Can miRador provide some test data? which will allow users to get on with it quickly.

rkweku commented 3 years ago

Hello,

  1. Yes, miRador does require only one species be listed as a reference. The primary reason for this is due to the conservation analysis being specific to the species being input, though miRador does still assess all plant organisms in miRBase for similarities. Conservation should be output no matter the species, so long as there is enough complementarity.

  2. Unfortunately, no. I developed miRador about 2 years ago now and, as far as I am aware, sRNAanno did not exist at that time. Simply put, I used among the most comprehensive repositories that I could a the time, though I may try to add additional sources if I get the time.

  3. Not in its current state, no. Implementing this shouldn't be terribly difficult though so I will try to add this feature soon. Technically, this could be hacked by refining the miRNAs present in miRBasePlantMirnas.fa with your own set of miRNAs, but one would have to be careful when doing this because miRador expects miRNA names to be named with a particular format. This is one reason why I preferred the use of miRBase as the miRNA names are standardized and I know what to expect in the parsing of the data.

  4. Yes, this would be useful. Let me see if I can add some test data.