Research Area

Custom searches of the viral databases
Building new tools .
The genome annotation

Link @ http://athena.bioc.uvic.ca/

The research covers diverse areas of evolutionary biology, and molecular evolution in particular. It combines theoretical and empirical approaches, and particularly evolutionary inference from genome sequence data.

Links @ http://www.gen.cam.ac.uk/research/welch/GroupPage/Home.html

Address of the bookmark: http://samtools.sourceforge.net/swlist.shtml

Our Research Team prides itself on driving cutting edge, industrial-scale
science to make an impact that belies the team’s size, in an environment
and culture that fosters creativity, innovation, collaboration, and fun.

More than 80% of our customers consent to participate in research, and as
a result of their participation, we have one of the largest recontactable,
genotyped, and phenotyped research cohorts in the world. The scope and
breadth of our vision means that most of the methods and tools necessary
to unlock the potential of this unique resource for discovery have yet
to be developed.

Our science has garnered the respect of many members of the
broader scientific community. For a list of our publications, see
www.23andme.com/publications/for-scientists/.

Join us! Visit our Careers page (www.23andMe.com/careers) to learn more
about these open positions:

• Scientist, Research Communications
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pfontanillas@23andme.com

ABACAS, that is able to contiguate contigs from a de novo assembly against a closely related reference.

IMAGE, an iterative approach for closing gaps in assembled genomes using mate pair information. It is able to close gaps left open by the assembler in a draft genome, even when using the same data sets as used by the original assembler.

iCORN, that enables errors in the consensus sequence to be corrected by iteratively mapping reads to the current assembly. An improved version, especially correction Pacfic Bioscience assemblies (PacBio) can be found here.

RATT, a tool to transfer the annotation from a reference genome, or an earlier assembly, onto the latest assembly.

PAGIT bundles these software and makes them more accessible for users.

Address of the bookmark: http://www.sanger.ac.uk/science/tools/pagit

Disclaimer: This cartoon is solely designed to create humour and fun, not to offend any PI, supervisor or student.

For example, you can run a search in Assembly and use check boxes (see left side of screenshot below) to refine the set of genome assemblies of interest. Then, just open the “Download assemblies” menu, choose the source database (GenBank or RefSeq), choose the file type, and start the download. An archive file will be saved to your computer that can be expanded into a folder containing your selected genome data files.

More at https://ncbiinsights.ncbi.nlm.nih.gov/2017/05/08/genome-data-download-made-easy/

More at >> http://www.nottingham.ac.uk/deepseq/events.aspx

We describe a new method for predicting the ancestral order and orientation of those intervals from their observed adjacencies in modern species. We combine the results from this method with data from chromosome painting experiments to produce a map of an early mammalian genome that accounts for 96.8% of the available human genome sequence data. The precision is further increased by mapping inversions as small as 31 bp. Analysis of the predicted evolutionary breakpoints in the human lineage confirms certain published observations but disagrees with others. Although only a few mammalian genomes are currently sequenced to high precision, our theoretical analyses and computer simulations indicate that our results are reasonably accurate and that they will become highly accurate in the foreseeable future. Our methods were developed as part of a project to reconstruct the genome sequence of the last ancestor of human, dogs, and most other placental mammals;

Address of the bookmark: http://www.bx.psu.edu/miller_lab/car/