CONTRA: copy number analysis for targeted res... [Bioinformatics. 2012] - PubMed - NCBI

http://www.ncbi.nlm.nih.gov/pubmed/22474122
Bioinformatics. 2012 Apr 2. [Epub ahead of print]
CONTRA: copy number analysis for targeted resequencing.
Li J, Lupat R, Amarasinghe KC, Thompson ER, Doyle MA, Ryland GL,
Tothill RW, Halgamuge SK, Campbell IG, Gorringe KL.
Source
Bioinformatics Core Facility, Victorian Breast Cancer Research
Consortium Cancer Genetics Laboratory and Molecular Genomics Core
Facility, Peter MacCallum Cancer Centre, VIC 3002, Australia, 3Dept.
of Mechanical Engineering, Sir Peter MacCallum Dept. of Oncology, and
Dept. of Pathology, University of Melbourne, Parkville, VIC 3010,
Australia.
Abstract
MOTIVATION:
In light of the increasing adoption of targeted resequencing as a
cost-effective strategy to identify disease-causing variants, a robust
method for copy number variation (CNV) analysis is needed to maximize
the value of this promising technology.
RESULTS:
We present a method for CNV detection for targeted resequencing data,
including whole-exome capture data. Our method calls copy number gains
and losses for each target region based on normalized depth of
coverage. Our key strategies include the use of base-level log-ratios
to remove GC-content bias, correction for an imbalanced library size
effect on log-ratios, and the estimation of log-ratio variations via
binning and interpolation. Our methods are made available via CONTRA
(COpy Number Targeted Resequencing Analysis), a software package that
takes standard alignment formats (BAM/SAM) and outputs in variant call
format (VCF4.0), for easy integration with other next-generation
sequencing analysis packages. We assessed our methods using samples
from seven different target enrichment assays, and evaluated our
results using simulated data and real germline data with known CNV
genotypes.Availability and implementation: Source code and sample data
are freely available under GNU license (GPLv3) at
http://contra-cnv.sourceforge.net/

PLoS Genetics: Genetic Analysis of Floral Symmetry in Van Gogh's Sunflowers Reveals Independent Recruitment of CYCLOIDEA Genes in the Asteraceae

PLoS Genetics: Genetic Analysis of Floral Symmetry in Van Gogh's Sunflowers Reveals Independent Recruitment of CYCLOIDEA Genes in the Asteraceae

http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002628

Abstract Top

The genetic basis of floral symmetry is a topic of great interest because of its effect on pollinator behavior and, consequently, plant diversification. The Asteraceae, which is the largest family of flowering plants, is an ideal system in which to study this trait, as many species within the family exhibit a compound inflorescence containing both bilaterally symmetric (i.e., zygomorphic) and radially symmetric (i.e., actinomorphic) florets. In sunflower and related species, the inflorescence is composed of a single whorl of ray florets surrounding multiple whorls of disc florets. We show that in double-flowered (dbl) sunflower mutants (in which disc florets develop bilateral symmetry), such as those captured by Vincent van Gogh in his famous nineteenth-century sunflower paintings, an insertion into the promoter region of a CYCLOIDEA (CYC)-like gene (HaCYC2c) that is normally expressed specifically in WT rays is instead expressed throughout the inflorescence, presumably resulting in the observed loss of actinomorphy. This same gene is mutated in two independent tubular-rayed (tub) mutants, though these mutations involve apparently recent transposon insertions, resulting in little or no expression and radialization of the normally zygomorphic ray florets. Interestingly, a phylogenetic analysis of CYC-like genes from across the family suggests that different paralogs of this fascinating gene family have been independently recruited to specify zygomorphy in different species within the Asteraceae.

Author Summary Top

The evolution of flower shape and symmetry is of great interest to plant biologists, because it can affect pollinator behavior. Species in the flowering plant family Asteraceae exhibit flower heads that can contain both bilaterally and radially symmetric flowers. In this study, we identify a CYCLOIDEA-like gene that is responsible for determining flower symmetry in sunflower. Mis-expression of this gene causes adouble-flowered phenotype, similar to those captured in Vincent van Gogh's famous nineteenth-century paintings, whereas loss of gene function causes radialization of the normally bilaterally symmetric ray florets. Interestingly, this gene is not orthologous to the CYCLOIDEA-like gene responsible for floral symmetry in other members of the Asteraceae, providing evidence of the parallel recruitment of different members of the same gene family for the same function.

FAQ: Annotation of reads, Tophat, Galaxy

Another post by Jennifer that I feel is a frequently asked question that should be on a wiki somewhere.


---------- Forwarded message ----------
From: Jennifer Jackson

Hello,

The tools TopHat/Cufflinks will map and assemble transcripts from sequencing reads. This mapping give each component (short read, transcript, gene boundary) genomic coordinates with respect to the target reference genome.

Annotation is also mapped to the reference genome by genomic coordinates. This can be derived from different sources, a look at a genome browser project that focuses on annotation will help you to understand the concept. Good choices can be found under the Galaxy tool group "Get Data".

One way to merge the two (assign "annotation" to a "sequence/transcript/gene"), is to identify overlapping coordinate regions on the reference genome between the two. Please see the tools in the group "Operate on Genomic Intervals" and the associated wiki for help/choices http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations. Galaxy is a good resource for this type of analysis.

Another way to obtain annotation is to run annotation algorithms directly on the sequence data itself. This is a large and varied analysis space. The public main Galaxy server has some tools for this type of analysis and more are offered if you decided to run a local/cloud instance with repositories from the Tool Shed.
http://getgalaxy.org
http://wiki.g2.bx.psu.edu/Tool%20Shed

For annotation, it is best to know what you are looking for, perform some searches both within the web tools you prefer and with a search tool such as Galaxy, use that research to determine the best platform to use the tool, then sort out the technical details. For general technical 'how-to-use' help with Galaxy, plus some basic scientific operations, these are good places to get oriented/started:
http://wiki.g2.bx.psu.edu/Learn
https://main.g2.bx.psu.edu/u/james/p/exercises

Best,

Jen
Galaxy team

On 4/3/12 7:30 AM, hsharm wrote:
>
> Dear galaxy users,
> This might be a very basic question to most of you. But I was hopimg I
> could get better understanding of this concept by asking you all.
> How exactly can we accomplish annotation of our reads? The combination
> of Tophat and cufflinks does annotate genes right? . I am a bit confused
> regarding this topic. Any help will be much appreciated.
> Thanks.

___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

 http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

 http://lists.bx.psu.edu/

[Velvet-users] My "Velvet Advisor" web site to help beginners choose a k-value

A cool resource done by Torsten Seemann for a frequently asked question.
what k-value do I use?
Source: velvet mailing list

http://dna.med.monash.edu.au/~torsten/velvet_advisor/

It's aimed at beginners who want some guidance with choosing "k" and don't feel comfortable yet thinking in terms of k-mers rather than bases.

It hasn't been tested thoroughly, so will break if you give it silly input, but I think the basics work.

Hope you find it helpful!

--
--Dr Torsten Seemann
--Scientific Director : Victorian Bioinformatics Consortium, Monash University, AUSTRALIA

--http://www.bioinformatics.net.au/

_______________________________________________
Velvet-users mailing list
http://listserver.ebi.ac.uk/mailman/listinfo/velvet-users

Creating An NFS-Like Standalone Storage Server With GlusterFS 3.2.x On Ubuntu 11.10 | HowtoForge - Linux Howtos and Tutorials

This tutorial shows how to set up a standalone storage server on Ubuntu 11.10. Instead of NFS, I will use GlusterFS here. The client system will be able to access the storage as if it was a local filesystem. GlusterFS is a clustered file-system capable of scaling to several peta-bytes. It aggregates various storage bricks over Infiniband RDMA or TCP/IP interconnect into one large parallel network file system. Storage bricks can be made of any commodity hardware such as x86_64 servers with SATA-II RAID and Infiniband HBA.

http://www.howtoforge.com/creating-an-nfs-like-standalone-storage-server-with-glusterfs-3.2.x-on-ubuntu-11.10

R 2.15.0 is released | (R news & tutorials)

The build system rolled up R-2.15.0.tar.gz (codename "Easter Beagle") at 9:00 this morning. This is the first release of the 2.15 series and contains several new features and changes; see the list below for details.

You can get the source code from

http://cran.r-project.org/src/base/R-2/R-2.15.0.tar.gz

or wait for it to be mirrored at a CRAN site nearer to you.

Binaries for various platforms will appear in due course.

For the R Core Team

Peter Dalgaard
http://www.r-bloggers.com/r-2-15-0-is-released/

r twotorials: how to read an excel file (dot xls and dot xlsx) into a data frame with r

http://www.twotorials.com/2012/03/how-to-read-excel-file-dot-xls-and-dot.html