View Single Post
Old 04-02-2009, 01:48 PM   #21
RudyS
Member
 
Location: new york

Join Date: May 2008
Posts: 20
Default objective criterion for comparing de novo assemblies

The main issue is that there is no true objective criterion for comparing de novo assemblies when no close references are available.[/QUOTE]

Torsten

For your bacterial genomes the majority of the DNA is coding for proteins (presumably) ... long open reading frames for proteins that "make sense" is a decent biological criterion ... assembly errors will produce stop codons at a relatively high rate ... indels mostly lead to out-of-frame shifts more often than expected ... I have seen reports of people working on programs to incorporate this kind of CDS "spell-check" ... I do it with undergrads ...

Rudy
RudyS is offline   Reply With Quote