Recent Updates

Last post
Notes from the biomass will continue at nftb.net. My...
spitshine - 2006-07-16 13:11
Stubborn
OK, you got me. While technically not blogging at the...
spitshine - 2006-07-07 10:55
Greetings from another...
Greetings from another HBS-founder (media-ocean.de)....
freshjive - 2006-06-15 20:06
HBS manifesto will be...
Hi there! I am one of the hard blogging scientsts. We...
020200 - 2006-06-15 18:13
Latter posts - comment...
Things to do when you're not blogging: Taking care...
spitshine - 2006-04-29 18:46

About this blog

About content and author

A few posts of interest

The internet is changing... Powerpoint Karaoke
Quantifying the error...

Link target abbreviations

[de] - Target page is in German
[p] - Paywall - content might not be freely available
[s] - Subscription required
[w] - Wikipedia link
More...

Search

 

Archive

October 2005
Sun
Mon
Tue
Wed
Thu
Fri
Sat
 
 
 
 
 
 
 1 
 2 
 4 
 8 
10
13
15
16
17
18
19
20
22
24
26
27
28
29
30
31
 
 
 
 
 
 

Credits

The microbial pan-genome

Genomic sequencing of prokaryotes is now in a stage where it's no longer sufficient just to sequence the genome of a prokaryote with some relevance for publication in a good journal. You will have to come up with novel insights and either an interesting bug (getting rarer...) or sequence a bunch of related genomes. The latter was performed by a group at TIGR on Group B Streptococci, reporting that sequencing a few strains are not sufficient to represent all strains in the species.

From the abstract:
Analysis of these genomes and those available in databases showed that the S. agalactiae species can be described by a pan-genome consisting of a core genome shared by all isolates, accounting for approximately 80% of any single genome, plus a dispensable genome consisting of partially shared and strain-specific genes. Mathematical extrapolation of the data suggests that the gene reservoir available for inclusion in the S. agalactiae pan-genome is vast and that unique genes will continue to be identified even after sequencing hundreds of genomes.


Dr Ferfried Gutfind from the Barbara Cartland Center for Positivistic Genomics says: "The massive sequencing of six strains is a beautifully analyzed, yielding the surprising conclusion that species diversity in some niches will not be covered ever by traditional sequencing approaches. Even "classical" meta-genomics won't help to cover the sequence space in these organisms."
However, Noland Works, chairman of "Bioinformatics students against basically everything" concludes: "Yeah, roight, after sequencing six strains theses guys say that they need to sequence way more species to ever reach their goal in a contributed paper to PNAS. Sounds like setting up publications for references if you ask me." (I won't.)

See also the note in The Scientist.

Trackback URL:
https://binf.twoday.net/stories/1026152/modTrackback

Elsewhere...

Status

Online for 7161 days
Last update: 2006-07-16 13:11

Blogs
Conferences
Databases
Journals
Meta
Misc.
Papershow
Patents
PPI
Predictions
Publishing
The young PI
Useful tools
Profil
Logout
Subscribe Weblog