How To Extract Specific Long Non Coding Rna Family From Rfam 10.0 Database?

Question

[Hani]

Hi all,

How to extract specific long non coding RNA family from RFAM 10.0 database?

Thanks in advance..

Answer 1

[Paul Gardner]

Full length long ncRNAs aren't in Rfam. You're better off using another database for those eg. NRED, ENSEMBL or HGNC. The covariance models Rfam uses can't handle long or spliced sequences. Also repeats such as Alus do bad things to the BLAST pre-filters.

There are a few elements in Rfam that are lncRNA "domains". Eg. H19_1, H19_2, H19_3, KCNQ1OT1_1, Xist_exon1, ...

Ideally these would be available from the website using the 'types' annotation (SEARCH -> Entry Type). However, a lncRNA type hasn't been added yet. Perhaps in the next release.

[Hani]

how do i know which lncRNA structures are solved???

[Hani]

how do i know which lncRNA structures are solved experimentally???

[Paul Gardner]

What do you mean by 'solved' and 'experimentally'?

[Paul Gardner]

And 'structure'. Be specific please.

Answer 2

[Michael]

Like so: Got to the family, e.g.: http://rfam.sanger.ac.uk/family/snoZ107_R87 click sequences http://rfam.sanger.ac.uk/family/snoZ107_R87#tabview=tab2 Download.

[Michael]

I overlooked the long...