Subject: Software for analysis of repetitive DNA
Many of you are familiar with the Pythia server which began its service
to the community five years ago. Originally, the server was running
an Alu classification program implemented by Pat Monardo who worked
with me at that time (now at Cold Spring Harbor Laboratory).
The server was installed by Aleksandar Milosavljevic who arranged generous
computer support from the University of California, Santa Cruz (UCSC),
where he completed his PhD Thesis shortly after joining my team in 1990.
Thanks to the support from the US Deparment of Energy our group
developed basic software for identification of complex
and simple repetitive elements, including relevant databases of
repeats. Since 1992 this software has been running at Argonne National
Laboratory, where Aleks assumed a new position. Aleks continued to
improve Pythia, but a major effort is necessary to match growing
public demand from various sequencing labs.
Today, I would like to announce a major software addition to Pythia,
called CENSOR, which should speed up and facilitate identification,
analysis, annotation and removal (censoring) of repetitive DNA from
your sequences (ref. 1). CENSOR can process any human/primate
sequences as long as you put them in the IG/Stanford format
(currently used by Pythia), and use Subject:censor at the top
of your file. For details send "help" message to Pythia at anl.gov.
Please, try it and let us know your impressions.
email jurka at gnomic.stanford.edu
Reference: Jurka, J., Klonowski, P., Dagman, V., Pelton, P.
CENSOR - a program for identification and elimination of repetitive
elements from DNA sequences. Computers and Chemistry (1995, in press).