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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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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