Frequently Asked Questions about the ASmiR

1. What is the ASmiR?

2. How to acquire the AS region information and other information through a gene name, chromosome, genome coordinate, GO terms and gene function?

3. How to obatin the whole AS region information of a specie?

4. Can I view the miRNA target sites locating at the AS region?

5. Can I view the miRNA target sites locating at the whole Genome?

6. What is the most direct way to predicte the miRNA target sites of my own miRNA?

7. I would like to see the visulization AS region and miRNA target sites. Is this possible?

8. Can I locate a specific coding sequence, protein sequence and AS sequence on ASmiR?

9. Why are some genes missing from the search item of gene name in the homepage?

10. How do I download ASmiRdb data?

11. What are the tools and raw data you have used in ASmiR?

12. Why timed out has occurred when trying to submit the miRNA in the ASmiR_predition?




1. What is the ASmiR ? Back to top

  AsmiR is a comprehensive database and web server for deposition and identification of miRNA target sites locating at AS region from linear RNAs and alternative back-splicing from circular RNAs according to up-to-date PacBio-generated full-length isoform sequencing and Illumina sequencing from eleven plant species.


2. How to acquire the AS region information and other information through gene name, chromosome, genome coordinate, GO terms and gene function? Back to top

  We construct a keyword search system. You cam using gene name, chromosome, genome coordinate, GO terms and gene function as query condition on the middle search box of ASmiRdb homepage.



Then, you should chose the different query conditions



3. How to obatain the whole AS region information of a specie? Back to top

  You can click AS in the ASmiRdb homepage. The screenshot below shows an example of bamboo.





4. Can I view the miRNA target sites locating at the AS region? Back to top

  Click ASmiRNA in ASmiRdb homepage menubar to view this information. An example is shown in the screenshot below. Click hyperlink in the third column to view detail information of this AS region. (e.g. Bamboo):.



5. Can I view the miRNA target sites locating at the whole Genome? Back to top

  Of course, Click MiRNA_target in ASmiRdb homepage menubar to view this information. An example is shown in the screenshot below. Click hyperlink in the third column to view detail information of this AS region. (e.g. Bamboo):




6. What is the most direct way to predicte the miRNA target sites of my own miRNA? Back to top

  We develop a submission system. You can submit your own miRNA to our online submission.


7. I would like to see the visulization of AS structure and miRNA target sites. Is this possible? Back to top

  We visualize the AS structure and miRNA target sites. You can derive it easily from the top menubar (accessed via ASmiRdb top menubar -> Jbrowse)


  A screenshot of a typical AS structure and miRNA target sites are shown below. To view the actual structure, paste AS region into the Search box Where the red arrows indicate. (e.g Chr10:19172505-19172540 Populus trichocarpaV3)



8. Can I locate a specific coding sequence, protein sequence and AS sequence on ASmiR? Back to top

  Yes, you can accomplish by using the blast tool. BLAST analysis with datasets that include genomic sequence, coding sequence, protein and AS sequence. Available from the top menubar(accessed via ASmiRdb top menubar -> Blast).


9. Why are some genes missing from the search criteria of gene name on the homepage? Back to top

  We were not able to incorporate some genes without AS evets in this table. You can access it directly using this url:http://www.forestrylab.org/bioinfor/db/ASmiR/EtractSeq/xxx/ where Xx is the species abbreviation.


10. How do I download ASmiRdb data? Back to top

  We have a "Downloads" page, accessible from menubar of About ASmiR on the ASmiRdb home page. Or, access it directly using this url: http://www.forestrylab.org/bioinfor/db/ASmiR/download.php On this page you will find:


11. What are the tools and raw data you have used in ASmiR? Back to top

  You can also find those information from menubar of About ASmiR on the ASmiRdb home page. Or, click here


12. Why timed out has occurred when trying to submit the miRNA in the ASmiR_predition? Back to top

  Likely reasons include: too large miRNA submit; or the net environment is bad. Solutions: