how to download only viridiplantae miRNA from miRBase.

Question

[dinesh]

Hi, community

tell me how to download only viridiplantae miRNA from miRBase.

[Pierre Lindenbaum]

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] " ...

[dinesh]

its about downloading plant microRNAs from miRBase......

Answer 1

[komal.rathi]

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.

[dinesh]

thank you komal rathi sir for ur informative explanation....can you tell me how to remove redundancy from microRNAs

[komal.rathi]

What kind of redundancy? Can you post an example? And by the way, you are misgendering me :)

[dinesh]

sorry madame.....like duplicate sequences in miRNA reference set

[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.

[bdubay]

Hi, If it's not too late, can you please reshare the above list?

Answer 2

[prp291]

It is too late but I hope this blog post will help you