Hi Tiago,
Have tried out 'RNA & DNA Folding Applications' available on Prof. Michael Zuker's web server.
http://www.bioinfo.rpi.edu/applications/mfold/
Regards
P.Elango
International Crops Research Institute for the Semi-Arid Tropics (ICRISAT),
Patancheru - 502 324, Andhra Pradesh, India.
Work: +(91) 40 307 13321 , Home: +(91) 40 559 98770 / +(91) 98854 98770 (Mobile)
pelango at cgiar.org www.cgiar.org elango at palchamy.com
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Today's Topics:
1. Stem Loop detection (Tiago Antao)
----------------------------------------------------------------------
Message: 1
Date: 8 May 2006 08:12:24 -0700
From: "Tiago Antao" <tiagoantao at gmail.com>
Subject: [Bio-software] Stem Loop detection
To: bionet-software at moderators.isc.org
Message-ID: <1147101144.803247.232030 at j33g2000cwa.googlegroups.com>
Content-Type: text/plain; charset="iso-8859-1"
Hi!
I am trying to find documentation (a paper) on algorithms for Stem Loop
detection. Especially for detection in long sequences (in our case
whole mitochondrial genomes ~17kbp). I have searched in the usual
places (scholar.google.com, pubmed) but I only find algorithms for
secondary RNA structure detection which, in most cases, are
computationally intensive and not suitable for large sequences.
I also know that GCG has stem loop detection. Does anyone know if the
implemented algorithm is suited for long sequences (again ~17kbp)?
Many thanks,
Tiago
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