Genome sequencing without assembly / A technology in pre-sequencing process

February 15, 2012

In Advanced Sequencing Technology Awards 2011, Shendure, Jay Ashok of University of Washington, Seattle, got a grant, “Massively Parallel Contiguity Mapping” last year.

1) a method for shattering genomic DNA with symmetric tags that post hoc inform the ordering of adjacent fragmentation events in a way that is entirely independent of the primary sequence content;

I do not understand the detail, but I imagined the concept and made figure below.
Tags inserted into DNA for contiguity information

The above strategy will enable,
1) We do not need complex assemble processes.
2) We can make a genome sequence without problems on repeated sequences.
3) We can get each haploid information separately. We can apply this technology to polyploid organisms like wheat.

A problem to be expected is multiple inserted tags.
A reconstruction error caused by multiple inserted tags

When they complete the project and the technology is available, genome science will be renewed.

I have added SNS buttons and SNS commenting system

January 24, 2012

I have added SNS buttons including a Facebook Like button and a Google +1 button on the articles. I have used DISQUS commenting system for discussion.

Twitter clients with Bayesian classification?

May 9, 2010

I need filtration to read tweets by keywords and Bayesian classification. Could you suggest me any client with these functions? Especially welcome if they can filtrate expanded information from links in tweets and they work on a server as CGI, or something like it.

I found a related article:
Improving Twitter with a Bayesian filtering client

I’m very interested in the comment by Ian Mercer, but not found any related article in his site.

Python libraries for Bayesian classification

Python libraries for Twitter API

Biological symmetry: Pattern in coats in cats and dogs

May 3, 2010
  • Animals have symmetry like in zebra coat.
  • Some kinds of cats have symmetry in their coat.
  • The other cats and most dogs have asymmetry.
  • What is the mechanism making symmetry in their coats?
  • Tortoiseshell cats have asymmetry caused by their genes linked on X chromosome inactivated, which is known as X-inactivation.

It is well known that most wild animals have symmetry, like in zebra coat.

(from Wikipedia)

In tortoiseshell cats, they have genes related to the two coat colors linked to X chromosomes in the manner of hetero. One of X chromosomes is inactivated randomly in the cells at a stage of their development. If they are female, genes determining one coat color, black, are activated, and another color was suppressed by X-inactivation. It makes a colored patch, since the cells derived from it maintain inactivation of the X chromosome. Almost all tortoiseshell cats are female, since male have only one X chromosome and genes for one color.

(from Wikipedia)

I have heard from a manager of a pet shop that some kind of cat have symmetry in body coat pattern,  but pattern of most dogs could be asymmetrical in male and female.

What is the mechanism making asymmetry in male dogs? That may be not caused by X-inactivation. Asymmetry in body coat colors of cats and dogs could be related to the domestication by human. What are the molecular and genetic mechanism involved in making symmetry of body pattern in wild animals?

Reconstruction of time lines in Twitter / Confidential communication is possible in Twitter ?

April 26, 2010

Suppose Mr. foo and Ms. bar communicate each other in Twitter, and

1.If they use @foo or @bar in their Tweets, the others can reconstruct their time line, from their Tweets.
2.If they do not use @ and it is well known that they followed each other, then the others can reconstruct the time line,.
3.If they do not use @ and nobody know that they are following, then it may be difficult to reconstruct the time line by the others. Is that possible ?

In the 3rd case, Tweets may be able to use as a confidential communication between foo and bar, especially when they are not following each other.

My first post

April 4, 2010

I set basical items on my blog. Some plugins needed to be installed and tuned.

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