nsaunders does a tag cloud on journal feeds

August 25, 2008 at 2:42 am (bioinformatics, genome, tips) (, , )

Always found tag clouds useful when looking for interesting things on a blog.. but never thought of using wordle on journals to get a feel on what’s currently hot in a journal.. Nice one !

check his post here

going to try the same thing on journals i read frequently and update this post


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Lest you think annotation is easy

April 17, 2008 at 9:53 am (bioinformatics, genome, review) ()

Fungal Genomes and Comparative GenomicsLest you think annotation is easyApr 13
I love the title of this post. And I totally agree.. gene annotation is anything but easy..
keeping track of which prediction programs and the rationale behind the annotation (manual or automated) is one thing the author didn’t mention.

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Bioinformaticians needed!

April 9, 2008 at 5:06 am (bioinformatics, genome) (, )

Chanced upon an ad by the Rubin’s lab. at newscientist link

the job scope is largely similar to what I am doing now. Currently where i am, bioinformaticians are moving away from the industry. Sad but true.

perhaps if we need more directors here like

‘Director David C. Page likens the Institute to an artists’ colony. “What we do here at Whitehead is attract the best possible intellectual capital and empower maximally creative—really wildly creative—individuals to realize their dreams within these walls”.’

I love reading job descriptions in my field. They let u in on the developing areas where talent is needed, so you know where to improve yourself. I am surprised though they didn’t mention python.


• Develop and implement existing and new computational methods and tools for high-throughput analysis of diverse data.
• Integrate multiple types of data and analytical methods in creative ways to exploit genomic information such as gene expression profiles and large-scale genome sequence data
• Manage data handling and analysis pipeline for Solexa sequencing platform – use software and databases to assemble and analyze genome sequence data
• Assist with the design and development of major bioinformatics-related programming projects.
• Conduct independent research projects, including primary responsibility for authoring manuscripts for publication in biology and bioinformatics journals.
• Write custom scripts to access databases and analyze sequence data.
• Collaborate with and support lab personnel in the area of bioinformatics analysis.


• M.S./Ph.D. or equivalent in bioinformatics / computational biology disciplines with emphasis on biology.
• Minimum of one year of related experience.
• Proven experience using bioinformatics to solve biologically important questions.
• Experience with microarray data analysis, familiarity with online bioinformatics tools and databases, and pathway analysis.
• Experience with genome sequence alignments, large scale sequence data analysis
• Excellent interpersonal, verbal, and written communication skills.
• Must demonstrate outstanding personal initiative and the ability to work effectively as part of a team
• Background in utility programming (C Shell, Perl, JAVA, or other languages) in a UNIX environment, preferred but not required.
• Familiarity with designing, developing, and programming databases (Oracle, MySQL), preferred but not required.

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De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer.

March 17, 2008 at 6:51 am (genome, journal, sequencing, software) (, , )

 Chanced upon this interesting paper!

De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer.

Geneva University Hospitals;

Novel high-throughput DNA sequencing technologies allow researchers to characterize a bacterial genome during a single experiment and at a moderate cost. However, the increase in sequencing throughput that is allowed by using such platforms is obtained at the expense of individual sequence read length, which must be assembled into longer contigs to be exploitable. This study focuses on the Illumina sequencing platform that produces millions of very short sequences that are 35 bases in length. We propose a de novo assembler software that is dedicated to process such data. Based on a classical overlap graph representation and on the detection of potentially spurious reads, our software generates a set of accurate contigs of several kilobases that cover most of the bacterial genome. The assembly results were validated by comparing datasets that were obtained experimentally for Staphylococcus aureus strain MW2 and Helicobacter acinonychis strain Sheeba with that of their published genomes acquired by conventional sequencing of 1.5 – 3.0 kb fragments. We also provide indications that the broad coverage achieved by high throughput sequencing might allow for the detection of clonal polymorphisms in the set of DNA molecules being sequenced.

PMID: 18332092 [PubMed – as supplied by publisher]

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Consolidated quotes on junk DNA aka Non coding sequences

March 11, 2008 at 11:20 am (evolution, genome, junk dna, review) (, , , , , , )

check out this compilation of quotes on the genomicron blog

here’s a snapshot dated today his post will be updated. Go back to his post for updates!

To facilitate access to the series of posts on what has been said in the literature about noncoding DNA and its potential functions, I will maintain an updated list here.

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Supramap a tool to map evol trees onto a globe

March 3, 2008 at 9:44 am (bioinformatics, genome) (, , , )

interesting note to self should explore this one day..

http://supramap.osu.edu/supramap/index.php?page=theory — Geographic mapping of evolutionary trees projected into a virtual globe allows users to analyze the spread of the organismal lineages into areas of interest. When all these data are integrated, we can visualize patterns in or to develop and test hypotheses. For example, we have used supramap to combine phylogenetic and virtual globe technologies to pinpoint which strains of a virus are infecting which hosts in specific areas (Janies et al., 2007). Finally, because phylogenetic analysis groups like strains into lineages, information drawn from limited experimentation on one strain in a lineage can be used to predict the properties of another strain in the lineage. This transitive property of phylogenetic inference will help us predict which strains are capable of infecting humans, are pathogenic, and/or are resistant to drugs. These capabilities are valuable to the public health community to make informed decisions on where and how to allocate resources to prepare for emerging diseases.

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Next Gen sequencing technology

February 15, 2008 at 9:00 am (bioinformatics, funny, genome, sequencing) (, , , )

Just read the above post.. i liked his succint observation summarised below.
There has been almost no mention at this whole meeting of things related to function of genes. For example, I have not heard “gene ontology” once. I do not think I have even heard “annotation” once. Function and process have been replaced by terms like “systems biology” and “SNPs” and “networks” and “massively parallel.
haha I am just beginning to grasp the annotation part of the genome business and I can tell you its no joke.

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Artemis: a DNA sequence viewer and annotation tool

February 4, 2008 at 9:32 am (artemis, genome, java, software) (, , , )

screenshot of artemis in actionthere are so many tools for molecular biologists out there. that its not surprising to find a hidden gem that’s how i feel about artemis.

check it out! I think its invaluable for sequence annotation

artemis page

perl scripts to work with embl files

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50 million personal genome sequences by 2015?

January 7, 2008 at 5:29 am (genome) ()

Jason Bobe makes an estimate that there will be 50 million personal genome sequences by 2015. What do u think?


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