Be critical

Couple of interesting articles in the current issue of Bioinformatics (vol. 21 no. 24).

Steven Salzberg and James Yorke point out that all
current assemblers generate misassemblies
, particularly when dealing with repeat regions.

Pernille Nielsen and Anders Krogh analyse the annotation
of 143 prokaryotic genomes
and find large numbers of errors – in some cases they claim 60% of genes have the wrong start codon.

I think these articles are not so much a criticism of software or methods – the limitations are well known, but a warning to biologists that they should not uncritically accept the contents of databases.