Genome Assembly – Discussion on Standardization of How to Represent Assembled ‘Genome’

A few days back, Heng Li opened up a new discussion on -

A proposal of the Grapical Fragment Assembly format

Introduction Almost three years ago, there was a lengthy discussion in the Assemblathon mailing list about a generic format for fragment assemmbly. The end product is the FASTG format. In the discussion, I have [...]

Posted on 28 July 2014 | 1:42 pm

In DALIGN Paper, Gene Myers Delivers a Major Blow to His Biggest Competitor

While Gene Myers was busy working on neural images of fruitflies, he noticed the bioinformatics land being taken over by search algorithm originating from a ‘competitor’. Now he comes back with an outstanding paper (DALIGN) to show why he is still the master.

That competitor of Gene Myers is none other than Gene Myers, [...]

Posted on 28 July 2014 | 1:23 am

How Does the Unix Diff Algorithm Work?

A link from stackoverflow says -

The basic algorithm is described in “An O(ND) Difference Algorithm and its Variations”, Eugene W. Myers, ‘Algorithmica’ Vol. 1 No. 2, 1986, pp. 251-266; and in “A File Comparison Program”, Webb Miller and Eugene W. Myers, ‘Software–Practice and Experience’ Vol. 15 No. 11, 1985, pp. 1025-1040. The algorithm was [...]

Posted on 25 July 2014 | 10:02 am



Don’t Send Your Kid to the Ivy League – Former Yale Professor

“The nation’s top colleges are turning our kids into zombies” says William Deresiewicz. His wiki profile describes him as -

Career

Academia In 1998, Deresiewicz joined the faculty of Yale University. He taught courses in modern British fiction, Great Books, Indian fiction, and writing, among other areas.[10] He left academia in 2008 to become [...]

Posted on 28 July 2014 | 3:02 pm

A Beautiful Post – Fits Perfectly with our Theme of Decline of US Science

No End in Sight: Academic Research and “Time Off”

Here is the core, but entire article is worth reading.

I am a tenured professor working at a state university that has ceased to offer raises (including cost of living raises) to its faculty. When I started my job in 2007 I was making approximately $53,000, [...]

Posted on 25 July 2014 | 12:02 pm

UK Student Loans System near Collapse

Link

Inaccurate debt forecasting and a failure to collect student loans threaten the financial collapse of the UK’s student loans system; claim a group of MPs in a damning report.

The Business, Innovation and Skills Committee called for an urgent review of the system, saying the Chancellor’s removal of the cap on student numbers may [...]

Posted on 25 July 2014 | 8:47 am



BioXSD: the common data-exchange format for everyday bioinformatics web services

A paper on common standards came out in 2010 in Bioinformatics. It is being discussed in #socbin14 conference. Isn’t JSON more appropriate?

Motivation: The world-wide community of life scientists has access to a large number of public bioinformatics databases and tools, which are developed and deployed using diverse technologies and designs. More and more [...]

Posted on 12 June 2014 | 3:43 am

d3.js – Tutorials, Books, Examples

d3.js is a SVG-based framework.

1. mbostock/d3 github gallery

This is the best source for hands on learning and comes from the author of d3.js. There are many examples to choose from and study their codes. We have been going through those examples one by one.

————————-

2. Next you need quick tutorials. Please try [...]

Posted on 6 May 2014 | 11:28 am

We Plan to Be Early Adopters of Meteorchart

Earlier we talked about HTML5 and SVG, as well as kinetic.js, raphael and d3.js. Eric Rowell, the author of kinetic.js, developed a new program called Meteorchart, which seems interesting. We plan to use it for our bioinformatics applications.

The program is not free for everyone, but it has the type of license that we [...]

Posted on 3 May 2014 | 7:21 am



Benchmark Analysis of RNA-Seq is an Excellent Confirmation of ‘Short Read’ Noise

In the past, we talked about ‘short read noise’, which is the noise introduced by clean short reads due to being short. Readers may take at these two of our earlier commentaries for details.

End of Short-Read Era? – (Part I)

End of Short-Read Era? – (Part II)

An excellent biorxiv paper analyzing RNA-seq assemblies [...]

Posted on 16 July 2014 | 3:14 am

‘Transcriptome Assembly is Hard’, but Not Any More with Richard Smith’s Transrate

Richard Smith-Una, whose work was covered in our blog, releases a new quality assessment program (transrate) that we surely like to check out.

Transcriptome assembly is hard. The algorithms are complex, the data are messy, and it’s often not clear how to determine whether an assembly is suitable for answering a biological question.

Transrate [...]

Posted on 8 July 2014 | 7:53 am

Efficient Algorithms for de novo Assembly of Alternative Splicing Events from RNA-seq Data

Readers may enjoy this new arxiv paper from Gustavo Sacomoto (h/t: haldane’s sieve)

Efficient Algorithms for de novo Assembly of Alternative Splicing Events from RNA-seq Data

In this thesis, we address the problem of identifying and quantifying variants (alternative splicing and genomic polymorphism) in RNA-seq data when no reference genome is available, without assembling the [...]

Posted on 25 June 2014 | 8:21 am



Adam Smith and Theory of Evolution

What role did Adam Smith play in helping Darwin develop his theory of evolution? Quite a bit actually. If you think carefully, you will see many similarities between Adam Smith’s ‘The Wealth of Nations’ and Darwin’s theory of natural selection.

Adam Smith noticed that, in a pin factory, many less experienced workmen working together can [...]

Posted on 29 July 2014 | 3:22 pm

On the Mythology of Natural Selection

Evolutionary (adaptationist) explanations often do not follow any scientific principle and can be as hard to invalidate as religious explanation. For example, in a commentary in Science magazine titled How bird flocks are like liquid helium, we read -

The new model also predicts that information travels faster if the flock is well aligned—something else [...]

Posted on 29 July 2014 | 8:44 am

Stunning Siphonophore

What you see in the video is not one large animal, but a colony of individual animals. Each animal of the colony is specialized to do certain functions so that the colony acts like an entire body. So, they may shed light on evolution of complex multicellular body plans. More from wiki -

Siphonophores [...]

Posted on 29 July 2014 | 7:42 am



Non-random DNA fragmentation in next-generation sequencing

link

Next Generation Sequencing (NGS) technology is based on cutting DNA into small fragments, and their massive parallel sequencing. The multiple overlapping segments termed “reads” are assembled into a contiguous sequence. To reduce sequencing errors, every genome region should be sequenced several dozen times. This sequencing approach is based on the assumption that genomic DNA [...]

Posted on 10 June 2014 | 6:08 am

PacBio P4-C2, P5-C3, etc. – What Do They Mean?

We had been pondering about those cryptic terms and found by asking some people around that the P stands for polymerase and C stands for chemistry. Therefore, P4-C2 means polymerase of fourth generation and chemistry of second generation.

Polymerase

That got us curious about what the actual DNA polymerase sequences are for 2nd, 3rd or [...]

Posted on 4 April 2014 | 4:58 am

Three Amazing Applications of CRISPR/cas9

Changing genome in plants used to be incredibly difficult, but not any more. Here is an excellent review -

Plant genome editing made easy: targeted mutagenesis in model and crop plants using the CRISPR/Cas system

Targeted genome engineering (also known as genome editing) has emerged as an alternative to classical plant breeding and transgenic (GMO) [...]

Posted on 31 March 2014 | 9:58 pm



Early Evolution of Fish – A Primitive Fish from the Cambrian of North America

New Nature paper -

Knowledge of the early evolution of fish largely depends on soft-bodied material from the Lower (Series 2) Cambrian period of South China1, 2. Owing to the rarity of some of these forms and a general lack of comparative material from other deposits, interpretations of various features remain controversial3, 4, as do [...]

Posted on 12 June 2014 | 3:48 am

The Fishiest Story Ever – (ii)

This is a follow up of previous commentary – The Fishiest Story Ever – (i).

All orders of fish are shown below based on the following phylogeny (courtesy: Professor James Albert). Please note that we (humans, tetrapods) are also a part of the phylogeny tree shown below.

———————————————————— ———————————————————— ———————————————————— Argentiniformes

———————————————————— Salmoniformes

[...]

Posted on 7 May 2014 | 7:48 pm

Rare Megamouth Shark Caught in Japan

//

Source

Megamouth shark was first seen in 1976 and is so rare that -

According to WPTV, it was only the 58th megamouth to have been captured or sighted by man.

The Florida Museum of Natural History states that the first known capture of a megamouth shark was in 1976. It was [...]

Posted on 7 May 2014 | 7:38 pm



Immune System in Plants – A Good Review from 2011

We earlier posted on the possibility of LRR-type immune system of Ectocarpus. Readers may find the following review useful in that context.

Arabidopsis and the Plant Immune System

Notes.

1. The first challenge was to dispel the notion that Arabidopsis does have enemies.

2. Achievement in early (pre-genome) years -

The biggest accomplishment of these [...]

Posted on 8 July 2014 | 10:55 am

Bacterial Tricks for Turning Plants into Zombies

Here is another interesting paper along the same line as previous commentary. It was published by Saskia A. Hogenhout and colleagues, and we meant to cover it some time back, but did not get time.

Phytoplasma Effector SAP54 Hijacks Plant Reproduction by Degrading MADS-box Proteins and Promotes Insect Colonization in a RAD23-Dependent Manner

Pathogens that [...]

Posted on 16 May 2014 | 10:24 am

A gene horizontally transferred from bacteria protects arthropods from host plant cyanide poisoning

Elife published this interesting paper on co-evolution -

Cyanogenic glucosides are among the most widespread defense chemicals of plants. Upon plant tissue disruption, these glucosides are hydrolyzed to a reactive hydroxynitrile that releases toxic hydrogen cyanide (HCN). Yet many mite and lepidopteran species can thrive on plants defended by cyanogenic glucosides. The nature of the [...]

Posted on 16 May 2014 | 7:15 am



End Torture, Shut Down The CIA!

It is quite tragic that most Americans stopped standing for moral principles, but Ron Paul remains to be among the exceptions, as always.

End Torture, Shut Down The CIA! by – Ron Paul

Remember back in April, 2007, when then-CIA director George Tenet appeared on 60 Minutes, angrily telling the program host, “we don’t [...]

Posted on 29 July 2014 | 9:06 am

Next Stage of Economic War – China Raids Microsoft Offices in Beijing, Shanghai, Guangzhou and Chengdu

Maybe they cannot take Windows 8 any more.

From Reuters:

Microsoft targeted in apparent Chinese antitrust probe

(Reuters) – Microsoft Corp appears to be the latest U.S. company targeted by China for antitrust investigation as government officials paid sudden visits to the software firm’s Chinese offices on Monday.

Representatives from China’s State Administration for Industry [...]

Posted on 28 July 2014 | 8:42 pm

Conspiracy Theory Monday – Banned Books

Our readers know that we are full-fledged conspiracy theorist, as defined by “You Know You Are a Conspiracy Theorist If…” -

You are capable of critical thinking. You distrust mainstream media. You like nature. You think it’s a good idea to spend the Friday after Thanksgiving with your family rather than camping outside Best [...]

Posted on 28 July 2014 | 12:27 pm