[Bio-software] RE: Bio-soft Digest, Vol 12, Issue 5

Elango, Palchamy (ICRISAT-IN) p.elango at cgiar.org
Mon May 8 22:11:22 EST 2006

Hi Tiago,
Have tried out 'RNA & DNA Folding Applications' available on Prof. Michael Zuker's web server.

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"


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,


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