[BiO BB] need sugesstion

Indraneel Majumdar indraneel at indialine.org
Sat Jun 23 21:12:47 EDT 2001


Cancer bioinformatics work is being carried out in a few places like
ISREC (Switzerland) and CGAP (NCBI). These mainly are generating,
expression profiles, generalised sequence profiles, chromosome
aberration database etc. There are however lots of cancer databases
available on the net which are more suitable for browsing than for
automated retrieval systems. http://tumor.informatics.jax.org lists some
mouse tumour databases. Cancers are a specialised topic since the
dissimiliarity of oncogenes and normal genes would be very low. Hence
normal sequence search algorithms would probably not be able to detect
them easily while at the same time removing false positives. This is
just a guess but since you are working in the field you may wish to
check this out. I guess that a weighing scheme might be developed
specifically for carcinogenic sequences (based on already available
data) which might not only be able to detect a new possible carcinogenic
sequence but also detect an actual carcinogenic sequence a non-gene or a
suppressed gene. Detection of this might actually be vital to treatment
or prevention of the disease. Probably this would be most apparent in
common cancers so you might wish to start with colon cancer or leukemia
(which is often the last step).

best wishes,

On Thu, Jun 21, 2001 at 05:10:19AM -0700, nikhil gadewal wrote:
> Hi,
>     I am working as a scientific officer in a Research
> Institute working on cancers. I am postgraduated in
> Microbiology and accomplished with Bioinformatics
> course.
>     Thus my job is to apply my bioinformatics
> knowledge to the cancer field. I want some ideas i.e
> on which aspect of cancer...I can develop some
> databases, algorithm,sequence analysis etc.


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