Question: Novel miRNA identification
0
gravatar for tesic93
12 months ago by
tesic9310
tesic9310 wrote:

Hi!

What are some good open-licensed tools for novel miRNA identification from miRNA-Seq files? I've combed trough tools4mirs.org, but I haven't found something that suits my usecase, since most of them are either dependent on miRDeep2, which is licensed, or aren't quite what I need. I need a tool that has the following feartures:

  • can be used for human sequences

  • can identify novel mature miRNA sequences

  • can handle input read that have miRNA-Seq experimental strategy (but tools that can handle input files with other experimental strategies would be useful as well)

  • has a license that allows non-academic use of the tool

  • doesn't require usage of GUI

Thanks,

Nikola

ADD COMMENTlink modified 12 months ago • written 12 months ago by tesic9310

or aren't quite what I need

can you specify a bit more what your specific needs are?

ADD REPLYlink written 12 months ago by Friederike3.3k

Sorry, I should have been clearer with the question. I need a tool that can do the following:

  • can be used for human sequences

  • can identify novel mature miRNA sequences

  • can handle input read that have miRNA-Seq experimental strategy (but tools that can handle input files with other experimental strategies would be useful as well)

  • has a license that allows non-academic use of the tool

Thanks!

Nikola

ADD REPLYlink modified 12 months ago • written 12 months ago by tesic9310
1

you could edit your initial question to include all those details

ADD REPLYlink written 12 months ago by Friederike3.3k
1

Thanks, I've included that in the initial question.

ADD REPLYlink written 12 months ago by tesic9310

Aren't sRNAbench or CAP-miRSEQ suitable?

ADD REPLYlink written 12 months ago by h.mon24k

sRNAbench can't be downloaded from their website as far as I know, they had a server crash from which they didn't recover fully.

CAP-miRSEQ seems to use miRDeep2 for alignment, so I can't use it because of miRDeep's academic-only license.

ADD REPLYlink modified 12 months ago • written 12 months ago by tesic9310
1

Link to sRNAbench stand-alone jar:

http://bioinfo2.ugr.es/sRNAtoolboxDB/exec/sRNAbench.jar

ADD REPLYlink written 12 months ago by h.mon24k

Thanks! I'll try using sRNAbench then.

ADD REPLYlink modified 12 months ago • written 12 months ago by tesic9310
1
gravatar for Buffo
12 months ago by
Buffo1.4k
Buffo1.4k wrote:

miRDeep2 is probably the most common software to perform it.

ADD COMMENTlink written 12 months ago by Buffo1.4k
1

OP has indicated that that program is not suitable for their purpose due to licensing restrictions.

ADD REPLYlink written 12 months ago by genomax64k
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