2 answers
If you just want a list of Viridiplantae miRNAs, and the corresponding sequence, you can download the entire miRNA database file from here. The file is called miRNA.xls.gz and it looks like this:
Accession ID Status Sequence Mature1_Acc Mature1_ID Mature1_Seq Mature2_Acc Mature2_ID Mature2_Seq
MI0000001 cel-let-7 UNCHANGED UACA… MIMAT0000001 cel-let-7-5p UGA... MIMAT0015091 cel-let-7-3p CUA...
The ID column is the miRNA name, and the first three letters stand for the species. To get the three letter codes for all Viridiplantae species, you have to refer to another file in the same directory, it is called organisms.txt.gz and it looks like this:
zhvt VRL Herpesvirus of turkeys Viruses; 37108
peu PEU Populus euphratica Viridiplantae;Magnoliophyta;eudicotyledons;Salicaceae; 75702
eca ECA Equus caballus Metazoa;Bilateria;Deuterostoma;Chordata;Vertebrata;Mammalia;Laurasiatheria; 9796
ola OLA Oryzias latipes Metazoa;Bilateria;Deuterostoma;Chordata;Vertebrata;Pisces; 8090
bhv1 VRL Bovine herpesvirus 1 Viruses; 10320
csi CSI Citrus sinensis Viridiplantae;Magnoliophyta;eudicotyledons;Rutaceae; 2711
ccl CCL Citrus clementina Viridiplantae;Magnoliophyta;eudicotyledons;Rutaceae; 85681
crt CRT Citrus reticulata Viridiplantae;Magnoliophyta;eudicotyledons;Rutaceae; 85571
ctr CTR Citrus trifoliata Viridiplantae;Magnoliophyta;eudicotyledons;Rutaceae; 37690
You can search for all the Viridiplantae species (I think there are 73 species in total) and their corresponding three letter codes and then search those three letter codes in miRNA.xls file.
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komal.rathi
What kind of redundancy? Can you post an example? And by the way, you are misgendering me :)
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komal.rathi
I don't think there are any duplicates. You have to "show" some example. Don't just type. "Show" us what you are doing and what you want.
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komal.rathi
It is too late but I hope this blog post will help you
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How to download all plant noncoding RNAs (snRNA, rRNA, snoRNA, tRNA) from NCBI web page "How can I all download plant noncoding RNAs (snRNA, rRNA, snoRNA, tRNA) from NCBI web page. is that true? "Viridiplantae"[Organism] " ...
its about downloading plant microRNAs from miRBase......