ncRNA gencode files

Question

[kanwarjag]

In gencode how can I download ncRNA for GRCH37 ( (=comprehensive) gtf file I see GRCH38 are there but none of the link provided me the direction for GRC37/hg19 download

[GenoMax]

http://www.gencodegenes.org/releases/24lift37.html

[kanwarjag]

I downloaded standard (=comprehensive) it has- CDS; gene; mRNA; transcript; Start-codon; End_codon and Selenocystein.

Which one should be microRNA or ncRNA

Thanks

[Emily]

All of them will refer to all genes, coding or non. They should all have biotypes listed.

Answer 1

[natasha.sernova]

See this post.

A: ncRNA Vs miRNA

[kanwarjag]

Does that mean we have to process them seprately

[natasha.sernova]

There are many criteria, as they write in this post.

To try blastn - does it look hopeless or useless?

I saw also this page below. It doesn't tell me anything clearly about microRNA and ncRNA difference.

http://www.abcam.com/tag/non-coding%20rnas%20and%20micrornas

I found these 2 papers (see the right panel of the page for others):

Functional interactions among microRNAs and long noncoding RNAs.

http://www.ncbi.nlm.nih.gov/pubmed/24965208

Systematic transcriptome wide analysis of lncRNA-miRNA interactions.

http://www.ncbi.nlm.nih.gov/pubmed/23405074

and this DB:

lnCeDB: database of human long noncoding RNA acting as competing endogenous RNA

http://www.ncbi.nlm.nih.gov/pubmed/24926662

– it may be useful. You can get rid of lnc-RNAs, or at least recognize them.

And if nothing helps, try Biomart - it contains a lot of human sequence information.

See this post C: GC content calculation

and Biomart URL Devon gave (at the bottom).

MY SUGGESTION: IS IT POSSIBLE TO PREDICT micro-RNAs?

There is a site https://sites.google.com/site/mirnatools/mirna-databases

I am not sure it is free, but we can try...

List of RNA structure prediction software

https://en.wikipedia.org/wiki/List_of_RNA_structure_prediction_software#Inter_molecular_interactions:_MicroRNA:UTR

Question_biostars: How can I detect lncRNA?

How can I detect lncRNA? AND Is there any specific quality metrics for lncRNA-seq or miRNA-seq?

And also this site:

http://www.abcam.com/kits/microrna-database-and-target-predictor-resources

[natasha.sernova]

You asked this question for mouse. Is it impossible to repeat the same action for humans?

ncRNA mouse file from UCSC or other source

This question was about downloading all mirna from two databases.

How to download all miRNA sequences from ensembl and ucsc?

[kanwarjag]

mouse/ human should be OK. Thanks for detailed reply