Finding Ultraconserved elements between human and zebrafish

Question

[ddowlin]

Hi all,

I am looking to find ultraconserved elements between human and zebrafish. I understand multiple genomes (including these species) have already been aligned and ultraconserved elements have been identified. For example Miller et al. 2007.

Is there a website where I can download a list of ultraconserved elements found in two species? Ideally with some additional information such as genomic location and percentage identity.

Thanks in advance.

Miller et al . (2007) 28-Way vertebrate alignment and conservation track in the UCSC Genome Browser. Genome Research. doi: 10.1101/gr.6761107

[GenoMax]

Have you seen this: http://bioinformatics.bc.edu/chuanglab/cneViewer/

[BDK_compbio]

check this new paper http://www.cell.com/molecular-plant/abstract/S1674-2052(17)30166-1

Answer 1

[Chirag Nepal]

You can download/browse the conserved elements between human/zebrafish from ANCORA browser maintained by Lenhard's group. http://ancora.genereg.net/

You can select multiple CNEs based on similarity of 100%, 90%, 80% and so on.

[ddowlin]

Thanks for the suggestion. I have a follow-up question. Do you know how to download all conserved elements as a single table at once? So far, I can only select specific elements from the browser and download them individually.

[GenoMax]

Files are available for download at Ancora. See an example folder: http://ancora.genereg.net/downloads/danRer10/vs_human/

HCNE location files are named

HCNE_asm1_asm2_Xpc_Ycol.bed.gz

where asm1 and asm2 are identifiers for the compared genome assemblies, X is the percent identity threshold used for HCNE detection and Y is the number of alignment columns (window size) over which percent identity is computed

[Chirag Nepal]

Not sure, try with wget. Or contact the authors.