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

Insane Decision of the Day – Broad Institute Gets $650M to Cure Insanity !!

Over the last few months, I have been working on a rebuttal paper in the field of genetics + psychology and found an unbelievable number of garbage papers from well-known universities. After carefully pondering about what was going on, I came to the conclusion that too much money had been chasing too few ideas in [...]

Posted on 24 July 2014 | 10:29 pm

‘Epigenetics’ Explained, in the Context of Descendants of Holocaust and Slavery Victims

A renowned psychologist asked us by email:

It has been posited that the trauma involved in genocide has altered gene expression not only of Holocaust survivors (as well as descendents of African slaves and conquered Native American) but of their descendents. is there any theoretical or empirical basis for that proposal?

We are posting the [...]

Posted on 23 July 2014 | 2:36 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

University of Dundee Introduced Voluntary Severance Scheme, Compulsory One Next?

University of Dundee is among UK’s top educational institutions.

The University of Dundee (abbreviated as Dund. for post-nominals) is a public research university based in the city and Royal burgh of Dundee on the east coast of the central Lowlands of Scotland. It is consistently ranked within the Top 200 universities in the world and [...]

Posted on 25 July 2014 | 8:40 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



A Textbook-free ‘Introduction to Biological Anthropology’

Holly Dunsworth at Mermaid’s tale blog put together an wonderful commentary with free and online materials. Her audience is anthropology students, but others can also benefit from the materials on evolution. Especially, pay attention to unit 2.

Here are the topics. You can access the links from her blog post.

Unit 2. Explaining the similarities [...]

Posted on 23 June 2014 | 11:12 pm

A single female-specific piRNA is the primary determiner of sex in the silkworm

Link

The silkworm Bombyx mori uses a WZ sex determination system that is analogous to the one found in birds and some reptiles. In this system, males have two Z sex chromosomes, whereas females have Z and W sex chromosomes. The silkworm W chromosome has a dominant role in female determination1, 2, suggesting the existence [...]

Posted on 28 May 2014 | 5:00 pm

Sponge Jelly Genome is Studied to Find Evolutionary Origins of Neural Systems

Two months back, we mentioned about an upcoming paper, where Friday Harbor lab was a collaborator (“Animal Ancestors – Sponges or Comb Jellies?“). It just came out in Nature today.

The origins of neural systems remain unresolved. In contrast to other basal metazoans, ctenophores (comb jellies) have both complex nervous and mesoderm-derived muscular systems. These [...]

Posted on 22 May 2014 | 9:05 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



This Guide Will Help You Predict the Outcome of Any Middle-eastern Conflicts

Source: zerohedge

Posted on 25 July 2014 | 9:49 am

It Was Always Russia vs United Front of Dying Empires

(the names of countries are from wiki).

Hitler:

Ottoman:

Napoleon:

What happens this time in the graveyard of empires?

Posted on 24 July 2014 | 10:00 pm

Rain in Seattle and MH17 Tragedy over Ukraine

After a number of beautiful sunny days, it is raining again in Seattle. Cloudy skies remind us that we are getting closer to winter every day.

What does that have to do with the plane crash in Ukraine? Simple. Here is the world map and you can see where Seattle is located, where Kiev is [...]

Posted on 23 July 2014 | 4:46 pm