At July 11, 2001, softberry.com introduced their promoter prediction
approach in this newsgroup. The message contained a comparison to our
promoter prediction tool PromoterInspector
(http://www.genomatix.de/free_services/) but they did not elucidate
the differences between the two approaches. Therefore we would like to
add some comments to their original message:
1. Going for promoters that can be mapped from 5'-COMPLETE cDNAs is
the undisputed best way to do it.
However, the posted approach has some intrinsic problems:
2. it is not able to detect new genes
3. promoters of genes will be missed or false because cDNAs are often
5' incomplete.
4. if they consider 3000 bps upstream of the ATG codon, false
predictions might be made in case of genes with non coding first exon.
Just to give one example out of many others:
The human RCC1 gene (D00591) was found to have 14 exons, 8 of which
(starting from the seventh one) code the RCC1 protein (Furuno N. et
al., 1991, MEDLINE: 92120669). The first 6 exons (about 23.000 base
pairs in length including the introns) are non-coding. See also
http://genomatix.gsf.de/accounts/Help_gems/full_length_cDNA.html
We analysed 3000bps upstream from the ATG of the genomic sequence of
the RCC1 with TSSW which predicted one promoter in that region.
5. softberry.com did not give any comments about false positive
predicions in their message.
6. PromoterInspector was designed to detect promoter regions in
anonymous sequences - without any annotation. It is an approach which
is neither meant nor attempts to find the exact and entire promoter
(which contains the TSS). What we have in mind with PromoterInspector
is going for promoters in the whole genome and pinning them down
approximately to a region to come in with other tools for detailed
analysis. Therefore, according to our unique prediction quality, a
combination of a tool to search for the TSS and PromoterInspector
might overcome the problems mentioned above.
Dr. Matthias Scherf
Genomatix Software GmbH
Landsberger Strasse 6
D-80339 Muenchen
http://www.genomatix.de
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