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Googling the Genome with TraceSearch

Fri, 2006-03-24 22:26 — Duncan

GoogleThe Wellcome Trust Sanger Institute news feed often has interesting stories that are well written by a dedicated team of professional journalists, just like the news stories in the journal Nature. The latest instalment of the news feed describes TraceSearch, Sangers "DNA search engine". The press release gives an easily digestible overview of SSAHA: a fast search method for large DNA databases which they liken to the search engine Google. An earlier press release on TraceSearch titled Around the world in 800 billion bases, describes just how big the trace database is getting.


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Fri, 2006-03-31 19:47 — Greg

SSAHA has been around for a

SSAHA has been around for a while now (2001), I'm curious why all the fuss now ? Is it the searchable trace archive ? If so, why would you want to search the trace archive and not the assembled genomes ? I'm missing something obvious...

On the topic of Google, they have been nominated for a Captain Hook Award (Bio Piracy). The justification is here:

For teaming up with J. Craig Venter to create a searchable online database of all the genes on the planet so that individuals and pharmaceutical companies alike can 'google' our genes - one day bringing the tools of biopiracy online.

Read the rest here. Of course Google + Venter == Pure Evil. Seriously, I doubt whether this will amount to anything real, there is a world of difference between searching HTML and DNA.


Fri, 2006-04-07 22:08 — maximilianh

and blat?

yes and I wonder no one mentioned blat? As far as I remember, blat and ssaha are not too different, ssaha is even openly copying one if its main speed-ups from blat (storing 11mers in memory)...