Genomic Medicine 2015 - From 20 - 23 July 2015, HoChiMinh City, Vietnam

 At 2015-02-27 03:17:45 AM - 

General questions about the conference:
Conference chair: Ly Le
 Mobile: +84906578836
 Address: School of Biotechnology, International University, Vietnam National University.
 Email: ly.le@hcmiu.edu.vn

Question about the conference program and proceedings:
Conference co- chair: Son Pham
 Mobile: +18584364073
 Address: Department of computer science and engineering - University of California San Diego.
 Email: spham@salk.edu

Question about website and submission:
Admin: Hoa Pham
 Mobile: +841226119992
 Address: Department of computer science and engineering, Etool.Me Group.
 Email: thaihoabo@gmail.com

If you have any question, please write the below !!!
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C-Sibelia support channel

 At 2017-07-18 06:22:08 PM - 



C-Sibelia helps in Comparing assemblies to a reference genome. As a result, you will get:

  • A VCF file that describes all the found variants
  • A circos picture visualizes all rearrangements

For your convenience, C-Sibelia also annotates and predicts the effects of these variants on genes using snpEff.


If you have any question of running this tool or any suggestion please feel free to ask in this channel. 
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Since one month, I am trying to run C-Sibelia using two mitochondria genomes size around 85 kb… Still waiting for results…is there is any problem now a days with this tool. Looking forward for your reply.thank you…with regardsVikas

Sibelia support channel

 At 2013-10-04 08:54:48 AM - 

Sibelia: A scalable and comprehensive synteny block generation tool for closely related microbial genomes.

Ilya Minkin, Anand Patel, Mikhail Kolmogorov, Nikolay Vyahhi, Son Pham. Sibelia: A scalable and comprehensive synteny block generation tool for closely related microbial genomes.

Sibelia will be presented at 13th Workshop on Algorithms in Bioinformatics (WABI2013) in Nice, Sophia Antipolis, France.

Arxiv version is available: http://arxiv.org/abs/1307.7941

If you have any question of running this tool or any suggestion please feel free to ask in this channel. 

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Release date: 3rd October 2013AuthorsIlya Minkin (St. Petersburg Academic University)Nikolay Vyahhi (St. Petersburg Academic University)Mikhail Kolmogorov (St. Petersburg Academic University)Ekaterina Starostina (St. Petersburg Academic University)Son Pham (University of California, San Diego)IntroductionThis package contains two programs:Sibelia -- "Sibelia" is a tool for finding synteny blocks in closely related genomes, like different strains of the same bacterial species. It takes a set of FASTA files with genomes and locates coordinates of the synteny blocks in these sequences. It also represents genomes as permutations of the blocks.C-Sibelia -- This tool is designed for comparison between two genomes represented either in finished form or...

SFselect

 At 2013-08-27 09:48:40 AM - 

SFselect is a method for classifying genomic regions evolving under positive selection, from those evolving neutrally

SFselect can be used in different ways:

1) Classify polymorphism data using a pre-trained general model that is robust to many different combinations of (s,t) values, while maintaining high power. Barring reliable knowledge of the selective sweep, we recommend using this option.

2)Classify polymorphism data using a pre-trained specific model that is most powerful for a given combination of (s,t) values. These specific models do not generalize as well for other (s,t) values. This option may be used given reliable knowledge of the selective sweep.

3)Classify polymorphism data using your own trained model. This option may be used given reliable knowledge of the demographic history.
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BFB support channel

 At 2013-08-18 08:57:48 AM - 

Breakage-fusion-bridge (BFB) is a mechanism of genomic instability characterized by the joining and subsequent tearing apart of sister chromatids.

When this process is repeated during multiple rounds of cell division, it leads to patterns of copy number increases of chromosomal segments as well as fold-back inversions where duplicated segments are arranged head-to-head.

This software (BFB) facilitates the analysis of BFB mechanism in genomes
Citation: http://www.pnas.org/content/110/14/5546.full

If you have any question of running this tool or any suggestion please feel free to ask in this channel. 

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- BFB supports two modes :+ Text mode : Submit a text data from text form+ File mode : Submit a big file. The system will notify when finishing. (Sign up or Login if you want to work with files.)Use it at http://etool.me/software/bfb