Gumby



Gumby solves the problem of identifying statistically significant evolutionarily conserved regions in pairwise or multiple DNA sequence alignments.

Features

- Generality: can perform phylogenetic shadowing (close species) and footprinting (distant species) with equal facility.
- No training data required; only one arbitrary parameter.
- Ranking of conserved elements by P-value.
- Identification of conserved elements of any size.

VISTA Server

Gumby conservation analysis is automatically performed when DNA sequences are submitted to the mVISTA server, and conserved regions are graphically displayed using RankVISTA. Precomputed whole-genome Gumby results based on pair-wise alignments are available as RankVISTA tracks on the VISTA Browser.

Download source

Please read the license agreement before downloading the source code for Gumby. The agreement permits non-commercial use only and does not permit redistribution.

Author    Shyam Prabhakar
Email      gumby at lbl dot gov

Download whole-genome conserved noncoding sequences
The whole-genome sets of conserved noncoding sequences described in [Prabhakar et al, Genome Res. 2006] and displayed on the Vista Enhancer Browser [Pennacchio et al, Nature 2006;444:499-502] can be found here.

The whole-genome sets of extremely conserved noncoding sequences described in [Visel et al, Nature Genetics 2008] can be found here.

Gumby has been used in

Axel Visel, Shyam Prabhakar, Jennifer A. Akiyama, Malak Shoukry, Keith D. Lewis, Amy Holt, Ingrid Plajzer-Frick, Veena Afzal, Edward M. Rubin, and Len A. Pennacchio.
Ultraconservation identifies a small subset of extremely constrained developmental enhancers.
Nature Genetics, accepted for publication.

Nottingham WT, Jarratt A, Burgess M, Speck CL, Cheng JF, Prabhakar S, Rubin EM, Li PS, Sloane-Stanley J, Kong-A-San J, de Bruijn MF.
Runx1-mediated hematopoietic stem cell emergence is controlled by a Gata/Ets/SCL-regulated enhancer.
Blood 2007; [Epub ahead of print]

Qian-fei Wang, Shyam Prabhakar, Sumita Chanan, Jan-Fang Cheng, Edward M. Rubin, Dario Boffelli.
Detection of weakly conserved ancestral mammalian regulatory sequences by primate comparisons.
Genome Biology 2007;8(1):R1.

Len A. Pennacchio, Nadav Ahituv, Alan M. Moses, Shyam Prabhakar, Marcelo Nobrega, Malak Shoukry, Simon Minovitsky, Inna Dubchak, Amy Holt, Keith D. Lewis, Ingrid Plajzer-Frick, Jennifer Akiyama, Sarah De Val, Veena Afzal, Brian L. Black, Olivier Couronne, Michael B. Eisen, Axel Visel, Edward M. Rubin.
In vivo enhancer analysis of human conserved non-coding sequences.
Nature. 2006;444(7118):499-502.

Qian-fei Wang, Shyam Prabhakar, Qianben Wang, Alan M. Moses, Sumita Chanan, Myles Brown, Michael B. Eisen, Jan-Fang Cheng, Edward M. Rubin, Dario Boffelli.
Primate-specific evolution of an LDLR enhancer.
Genome Biology. 2006;7(8):R68.

Shyam Prabhakar, Francis Poulin, Malak Shoukry, Veena Afzal, Edward M. Rubin, Olivier Couronne, Len A. Pennacchio.
Close sequence comparisons are sufficient to identify human cis-regulatory elements.
Genome Res. 2006;16(7):855-63.   ***primary reference for Gumby***

Ahituv N, Prabhakar S, Poulin F, Rubin EM, Couronne O.
Mapping cis-regulatory domains in the human genome using multi-species conservation of synteny.
Hum Mol Genet. 2005;14:3057-63.

Hughes JR, Cheng JF, Ventress N, Prabhakar S, Clark K, Anguita E, De Gobbi M, de Jong P, Rubin E, Higgs DR.
Annotation of cis-regulatory elements by identification, subclassification, and functional assessment of multispecies conserved sequences.
Proc Natl Acad Sci USA. 2005;102:9830-5.

Martin J. et al.
The sequence and analysis of duplication-rich human chromosome 16.
Nature. 2004;432:988-94.

Schmutz J. et al.
The DNA sequence and comparative analysis of human chromosome 5.
Nature. 2004;431:268-74.