Friday, November 28, 2008

Solexa, high accuracy with millions of 36bp reads

De-novo vs. mapping assembly

In sequence assembly, two different types can be distinguished:

1. de-novo: assembling reads together so that they form a new, previously unknown sequence
2. mapping: assembling reads against an existing backbone sequence, building a sequence that is similar but not necessarily identical to the backbone sequence

http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000139

Abstract

Whole-genome sequencing is a powerful technique for obtaining the reference sequence information of multiple organisms. Its use can be dramatically expanded to rapidly identify genomic variations, which can be linked with phenotypes to obtain biological insights. We explored these potential applications using the emerging next-generation sequencing platform Solexa Genome Analyzer, and the well-characterized model bacterium Bacillus subtilis. Combining sequencing with experimental verification, we first improved the accuracy of the published sequence of the B. subtilis reference strain 168, then obtained sequences of multiple related laboratory strains and different isolates of each strain. This provides a framework for comparing the divergence between different laboratory strains and between their individual isolates. We also demonstrated the power of Solexa sequencing by using its results to predict a defect in the citrate signal transduction pathway of a common laboratory strain, which we verified experimentally. Finally, we examined the molecular nature of spontaneously generated mutations that suppress the growth defect caused by deletion of the stringent response mediator relA. Using whole-genome sequencing, we rapidly mapped these suppressor mutations to two small homologs of relA. Interestingly, stable suppressor strains had mutations in both genes, with each mutation alone partially relieving the relA growth defect. This supports an intriguing three-locus interaction module that is not easily identifiable through traditional suppressor mapping. We conclude that whole-genome sequencing can drastically accelerate the identification of suppressor mutations and complex genetic interactions, and it can be applied as a standard tool to investigate the genetic traits of model organisms.

Lions


panmictic: Referring to unstructured (random-mating) populations.

http://www.biochem.northwestern.edu/holmgren/Glossary/Definitions/Def-P/panmictic.html

How genetically structured are lion populations?

The genomic legacy of the lion, Panthera leo—one of the world's most charismatic carnivores—was studied using a large multigenic dataset. Population genomics of 357 individuals from most of the major lion populations in Africa and Asia refuted the hypothesis that African lions consist of a single, randomly breeding (panmictic) population and provided insight into the lion's natural history (see Antunes et al., doi:10.1371/journal.pgen.1000251). The high population structure observed highlights the importance of preserving lion populations in decline as opposed to prioritizing larger-scale conservation efforts.

Image Credit: Photo of lion cubs from Laikipia District, central Kenya, by James Warwick (http://www.jameswarwick.co.uk).

http://www.plosgenetics.org/article/browseIssue.action?field=issue

Thursday, November 27, 2008

Python, domain-domain interaction

Python code to take in two files, a pfam lookup table and a domain-domain interaction file.

#!/usr/bin/python

# loadin loopkup table
f = open("pfam-table.txt", "r")
pfam = {}
while True:
line = f.readline()
if (not line):
break
line = line.rstrip()
cols = line.split()
if (len(cols) < 2):
break
pfam[cols[0]] = cols[1]
f.close()

# load data to normalize
f = open("tmp2-clean.txt", "r")
dict = {}
while True:
line = f.readline()
if (not line):
break
line = line.rstrip()
cols = line.split()
if (len(cols) < 5):
break

d1 = pfam[cols[0]] #domain1
p1 = cols[1] #protein1
int = cols[2]
d2 = pfam[cols[3]]
p2 = cols[4]

key = p1+'-'+p2
key2 = p2+'-'+p1
if dict.has_key(key):
dict[key]=dict[key]+d1+'-'+d2+';'
elif dict.has_key(key2):
dict[key2]=dict[key2]+d1+'-'+d2+';'
else:
dict[key]=d1+'-'+d2+';'
f.close()

for e in dict.items():
srcdest = e[0].split('-')
print srcdest[0], srcdest[1], len(e[1].split(';'))-1, e[1]

A loooong post on astrology :D

http://dragonpower.tribe.net/thread/81eb3143-6c18-4340-9b31-db7c2740f488
http://www.suzannewhite.com/new-astrology/PiscesPig.html

luxe (lks, lks)
n.
1. The condition of being elegantly sumptuous.
2. Something luxurious; a luxury.

The degree of permeability in the Pisces/Pig subject is so elevated as to cause him or her a real burden. This person feels more deeply than we do. Pisces/Pigs are gentle souls with unlimited ambition. They are sensualists who love luxe and care immensely for tradition and custom. I'd say without hesitation that the Pisces/Pig's biggest stumbling block is the modern world. He is old-fashioned and firmly rooted in time-honored ways. Shortcuts irritate the Pisces/Pig. Nicknames grate on his nerves. Gadgets bore him. Some people accuse this person of being a clinging vine in matters of the heart. It's fully understandable because the Pisces born Pig needs the security of full-time affection and tenderness in order to survive. Without fervent full time love, he feels shipwrecked and alone. He will go to great lengths to hang onto an object of desire. Nothing, for the Pisces/Pig, can replace true love. His sex drive is known for being a tad over the top but...

Famous Pisces Pigs - Andrew Jackson, Ed McMahon...

Good Compatibilities - Cancer Cat/Rabbit...


Aquarius Pig

http://www.suzannewhite.com/new-astrology/AquariusPig.html

There evolves from the blend of Aquarius with Pig a brash quality that borders on lumpishness. Perhaps the Pig's naturally pastoral, countrified side imitates Aquarius's openness. Or maybe the Aquarian subject picks excess sincerity from the Pig and becomes too direct. But whatever the mechanics, this subject comes up both bold and forward. These people are aggressively charismatic. They know how to attract crowds and please them. Love is of the utmost importance the this reckless creature. His whisperings are full of sensuous innuendo and promises of marvelous sexual surprise. But when the lights are low and he or she gets you into bed, you might be surprised at how UN surprised you are by the follow up which...

Famous Aquarius Pigs - Ronald Reagan, John McEnroe, Sonny Bono...

Good Compatibilities - Gemini Cat/Rabbit...



Lastly, Metal begets Water, groundwater trickling its way through layers of the Earth's ore. Water's color is blue. Its season is full-blown winter. Water is always moving, fluid, and mutational. In our bodies, water's influence affects our plumbing systems, the kidneys and the bladder. The ear, too, comes under the spell of Water. Hence people born in Water-ruled years are frequently musical. They pick up on everything. Be it good or bad, they never miss a vibe. Water-ruled creatures are always very sensitive and sometimes even mentally fragile. The downside of Water's influence, then, is a stressful nervousness. To balance that fidgety, squeamish, overly sensitive side, Water endows its subjects with the noblest quality of all, kindness and sympathy. Sometimes too permeable, the Water-ruled must take precautions against drowning in the chagrin of those they see as less fortunate than themselves.

Pisces (February 19-March 20).
Cancer (June 21-July 22).
Gemini (May 21-June 20).

Rabbit
* 29 January 1903 - 15 February 1904: Water Rabbit
* 14 February 1915 - 2 February 1916: Wood Rabbit
* 2 February 1927 - 22 January 1928: Fire Rabbit
* 19 February 1939 - 7 February 1940: Earth Rabbit
* 6 February 1951 - 26 January 1952: Metal Rabbit
* 25 January 1963 - 12 February 1964: Water Rabbit
* 11 February 1975 - 30 January 1976: Wood Rabbit
* 29 January 1987 - 16 February 1988: Fire Rabbit
* 16 February 1999 - 4 February 2000: Earth Rabbit
* 3 February 2011 - 22 January 2012: Metal Rabbit
* 2023 - 2024: Water Rabbit
* 2035 - 2036: Wood Rabbit
* 2047 - 2048: Fire Rabbit

Those following traditional Chinese astrology consider people born in the Year of the Rabbit to make ideal diplomats or politicians. In Chinese astrological thought, a "rabbit person" is graceful, cultured, well-mannered, articulate, talented, and ambitious. They are virtuous, reserved, and have excellent taste. Rabbit people are admired, trusted, and are often financially lucky. Although Rabbit people get along well with many people, at heart they are considered to be basically reserved creatures, and are only truly happy when engrossed in some sort of scholarly or intellectual activity. Rabbit people are considered too sensitive for the world around them; they are not able to thrive in competitive or aggressive environments, and are anxious when others force them to take risks. Their inner world is considered too delicate for unsettled or unpredictable situations, and they tend to create peaceful and comfortable atmospheres - like rabbit dens - instinctively. According to traditional Chinese astrology, this characteristic makes them very hospitable and attentive people, who take care of those around them.

http://en.wikipedia.org/wiki/Rabbit_(zodiac)


http://en.wikipedia.org/wiki/Pig_(zodiac)

* 30 January 1911 - 17 February 1912: Metal Pig
* 16 February 1923 - 4 February 1924: Water Pig
* 4 February 1935 - 23 January 1936: Wood Pig
* 22 January 1947 - 9 February 1948: Fire Pig
* 8 February 1959 - 27 January 1960: Earth Pig
* 27 January 1971 - 14 February 1972: Metal Pig
* 13 February 1983 - 1 February 1984: Water Pig
* 31 January 1995 - 18 February 1996: Wood Pig
* 18 February 2007 - 6 February 2008: Fire Pig
* 5 February 2019 - 24 January 2020: Earth Pig
* 2031 - 2032: Metal Pig
* 2043 - 2044: Water Pig

Someone born in the year of the Boar is usually honest, straightforward and a patient person. They are a modest, shy character who prefers to work quietly behind the scenes. When others despair, they are often there to offer support. This type of person is reserved with those they do not know too well, but as time passes and they gain confidence, those around them may discover a lively and warm-hearted person behind that mask of aloofness. Despite those born in the year of the Boar having a wide circle of friends and acquaintances, they have few close friends who understand them and share their inner thoughts and feelings. It is easy to put trust in Boars; they won't let you down and will never even attempt to do so. Such people simply want to do everything right according to social norms.[9]

http://en.wikipedia.org/wiki/Pisces_(astrology)

Pisces
Attribute
Likes Feeling appreciated, feeling loved, freedom, stability, mystical settings/enchantment, dreaming, having their input valued, being unique
Dislikes Feeling vulnerable, having no goals to move toward, feeling invalidated, being criticized, illiteracy, noisy scenes and displays, having no sense of structure
Ideal careers caring for the needy as in the fields of medicine or veterinary medicine [4] • anything related to the sea [4] • acting [4] • psychics or mystics [4] • religion [4] • cooking [4] • pharmacist
The Chinese equivalent is thought to be the gentle, diplomatic Rabbit, whose lunar month is 6 March - 4 April.[14]

http://en.wikipedia.org/wiki/Aquarius_(astrology)

Aquarius
Attribute
Ideal Careers Group leadership [13] • science and research [13] • astronomy [13] • computer technology, electronics or software engineering [13] • aviation [13] • electronic communication or broadcasting [13] • photography [13] • theater [13] • social services [13] • music [13] • Anything with Drama,Music,Art and Science.[13]
Likes Friendship [15] • freedom [15] • intellectual stimulation • camaraderie • surprises • companionship • feeling understood • emotional safety.
Dislikes jealousy, possessiveness, control, ego plays, pointless meetings, narrow-mindedness, being ridiculed, routines, inequality, being taken for granted.
The Chinese equivalent is thought to be the unpredictable, charismatic Tiger, whose lunar month is 4 February - 5 March. [30]


http://www.evolvingdoor.ca/zodiac/signsindex.htm
http://chinese.astrology.com/pig.aspx

youtube avril

Woke up to the sound of Avril's Innocence

http://www.youtube.com/watch?v=TDRT-bYRvMI



"This innocence is brilliant .... It's so beautiful, it makes me want to cry ... "

web idea

Woke up today with this crazy idea of letting someone know secretly that you like them. Probably inspired by the movie `Let the Love Begin`. The concept of a secret admirer, secret saviour you name it, is very enticing. Now there's already something similar called `Send Secret Thoughts ♥` but some people complains that it shows up when you post something, so we'll try to address that issue if possible in our own implementation muwhahahaha.

expert finder, contact, location, fields, etc

Tuesday, November 25, 2008

Jobs

http://www.bioinformatics.org/jobs/?show=archives

http://bioinformatics.biology.ualberta.ca/careers.html
Pharmaceutical Science

CheminformaticianChoose to put your hands to work in a lab or on a keyboard!
Pharmacogenetician
Pharmacogenomics

Applied Science

Structural analyst
Molecular modeler
Bio-statistician
Biomechanics
Database programmer

Life Sciences

Scientific Curator
Gene analyst
Protein analyst
Phylogeneticist
Research scientist
Research associate

Computer Science & Engineering

Database programmer
Software developer
Computational biologist
Network Administrator / Analyst

http://www.centennialcollege.ca/
http://www.senecac.on.ca/
http://www.bcgsc.ca/career/BCPNCB14-01-2008
http://www.bioinformatics.sfu.ca/
http://bioinformatics.ubc.ca/
http://www.zymeworks.com/
http://www.pathogenomics.bc.ca/brinkman/
http://www.bms.com/career/data/

Public Health Agency: FA10 - Bioinformatics Research Technician

BC Disease Control
http://www.bccdc.ca/util/about/UBCCDC/People/Faculty/default.htm

UBC Michael Smith
http://www.msl.ubc.ca/faculty

Community Living BC
clbc.humanresources@gov.bc.ca

CSIS National Headquarters, Ottawa (Ontario).http://csiscareers.ca/available-jobs/3

HootSuite: Social Media Management Dashboard

Antibody, bioinformatics blogs

Antibody tutorial
http://microvet.arizona.edu/Courses/MIC419/Tutorials/antibody.html

Monday, November 24, 2008

Darwin


http://darwin-online.org.uk/

The complete work of Charles Darwin, great scientist who pioneered the term 'evolution'.

Australia 2008

This movie looks interesting (starring Nicole Kidman and Hugh Jackman - Wolverine) ...
http://www.imdb.com/title/tt0455824/

The movie's about WWII in Australia I think.

" Set in northern Australia before World War II, an English aristocrat who inherits a sprawling ranch reluctantly pacts with a stock-man in order to protect her new property from a takeover plot. As the pair drive 2,000 head of cattle over unforgiving landscape, they experience the bombing of Darwin, Australia, by Japanese forces firsthand. "

Btw, just found out that New Zealand is actually South East of Australia and not somewhere in Europe -o-

DNA Day

In 2003 Congress designated April 25th as “DNA Day” to commemorate the completion of the Human Genome Project in April 2003, and Watson and Crick’s publication of the double-helix structure of DNA in 1953.

LET THE LOVE BEGIN


http://en.wikipedia.org/wiki/Let_the_Love_Begin

This movie was pretty good, didn't like the main heroine's acting that much but overall it was pretty funny and a happy ending :D Whenever I see love stories that has something about travelling, it reminds me of her, feeling guilty somewhat ...

http://www.lyricsdownload.com/kyla-let-the-love-begin-lyrics.html

The song (LET THE LOVE BEGIN by Jerome John Hughes And Kyla) for this one is awesome.