UCNEbase 2013, Ultra-Conserved Sequence Elements.

Description

Vertebrate ultraconserved sequence elements (UCNEs) from UCNEbase. The collection is offered: (i) as an oriented "regions" SGA file where positions on the + and - strand indicate the beginning and end of a UCNE, respectively, and (ii) as an unoriented SGA file where the positions indicate the center of a UNCE.

Source

Samples

From H. sapiens (Feb 2009 GRCh37/hg19).

Sequence-derived:

Filename Description Feature GEO-ID
1 ucne_hg19.sga UCNEs from UCNEbase UCNE -
2 ucne_hg19_c.sga UCNEs from UCNEBase UCNE -

Notes on samples:

The sixth field of the SGA files contains the name of the UCNE.

Technical Notes

The input BED file was converted into SGA and FPS format using custom Perl scripts available from the MGA ftp sitei (ftp://ccg.vital-it.ch/mga/). Chromosome name conversion and generation of the FPS files was done with chr_replace_sga.pl and sga2fps from ChIP-Seq v. 1.5.3.

References

Last update: 26 May 2017