Hello everyone
I did an experiment using microRNA NGS and because of lack of funds we did the alignment of microRNA against zebarfish microrna and I got some novel microRNA. Now I want to alignment of novel microRNA against the remaining species (vertebrate).
Which friendly tool should I use? How can I get only the vertebrate microRNA from mirbase?
Thanks a lot for your help.
There is functionality on the miRbase website similar to BLAST. Here's how you do it:
1) Click on "search" tab across the top and the page that opens is a search tool.
2) The last section is "Search by Sequence". Type in your novel zebrafish sequence in the textbox. You can also upload a file if that is preferable.
3) You can choose to search by mature miRNA or hairpin sequences. I get the sense that you'll want "mature miRNA".
4) Choose the search algorithm; in your case, it sounds like "SSEARCH" is the better option.
5) Under "show results only from specific organisms", use the taxonomy filter to select Vertebrates: Metazoa - Bilateral - Deuterosomia - Chordata - Vertebrata
6) Finally, click "search miRNAs".
Hope that helps!
Dear Adham Sabri,
to search Vertebrates go to
http://www.mirbase.org/cgi-bin/browse.pl
check the "Browse" link and open
Metazoa - Bilateria - Deuterostomia - Cordata - and Vertebrata.
Therein are Agnathostomata, Amphibia, Aves, Mammalia, Pisces and Sauria,
which are all linked to the respective species, example:
Mammalia - Primates - Hominidae - Homo sapiens (1881 precursors, 2588 mature) [GRCh38]
Have fun,
Dirk
There is functionality on the miRbase website similar to BLAST. Here's how you do it:
1) Click on "search" tab across the top and the page that opens is a search tool.
2) The last section is "Search by Sequence". Type in your novel zebrafish sequence in the textbox. You can also upload a file if that is preferable.
3) You can choose to search by mature miRNA or hairpin sequences. I get the sense that you'll want "mature miRNA".
4) Choose the search algorithm; in your case, it sounds like "SSEARCH" is the better option.
5) Under "show results only from specific organisms", use the taxonomy filter to select Vertebrates: Metazoa - Bilateral - Deuterosomia - Chordata - Vertebrata
6) Finally, click "search miRNAs".
Hope that helps!
I endorse the answer given by Mr. Warren Mcgee but the taxonomy filter doesn't allow you to go for the hierarchy of Vertebrates: Metazoa - Bilateral - Deuterosomia - Chordata - Vertebrata. You can directly chose the vertebrata under the category of metazoa
The provided link will directly bring you to the page for your desired alignments
http://www.mirbase.org/search.shtml
thanks a lot Mr.Iftekhar and Mr.Warren for your help. i looked in the search and i think u can submit one sequence and u cant submit a set of microrna in the search box.
- Badges
- Science topic
- Similar topics
- Biological Science
- Zoology
- Ichthyology
- Vertebrates