reading genomes, bit by bit

We want to be able to read a genome like a book. We are at a remarkable time in biology where at last we can see the source code for life — the complete genomic DNA sequences that specify development, regulation, and function of organisms — but, frustratingly, we are still far from adequately understanding how to read this vast trove of encoded information, and far from being able to reconstruct how it evolved. Our laboratory develops computational methods for genome sequence analysis, and in particular for identifying remote evolutionary relationships between distantly related protein and RNA sequences.

[more about our research projects...]



recent publications

A Probabilistic Evolutionary Model Compatible With Standard Affine Gap Cost Sequence Alignment. E. Rivas, S. R. Eddy. Manuscript submitted, 2013. [preprint]

Challenges in Homology Search: HMMER3 and Convergent Evolution of Coiled-Coil Regions. J. Mistry, R. D. Finn, S. R. Eddy, A. Bateman, M. Punta. Nucl. Acids Res., in press, 2013. [abstract] [reprint]

[more about our publications...]



software

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HMMER
Hidden Markov models for sequence
profile analysis.

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Infernal
RNA structure analysis using
covariance models.

[more about software we make available...]



databases

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Pfam
Database of protein family alignments
and hidden Markov models.

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Rfam
The Rfam database of RNA alignments,
consensus secondary structures,
and profile SCFGs.

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Dfam
The Dfam database of repetitive
DNA sequence elements.

[more about databases and servers we make available...]



how to reach us

HHMI Janelia Farm Research Campus
19700 Helix Drive
Ashburn, VA 20147, USA
Phone: 571.209.4000 [this is the general Janelia operator number, not an office]

[more about people in the lab and their contact info...]