Online Analysis Tools

Andrew M. Kropinski kropinsk at post.queensu.ca
Wed Mar 10 03:15:18 EST 2004

Online analysis tools (http://molbiol-tools.ca) has been updated to include:

1. DNA base composition analysis tool. Written by J. Zheng, (Queen's 
University, Canada) this program can analysis a 30 kb
DNA sequence in three different ways. It computes the percentage of one or 
two selectable nucleotide(s), the normal
skew of two selectable nucleotides, and the cumulative skew of two 
selectable nucleotides for a given sequence. The
result can be displayed in both graphic and value data format. Accessible 
from http://molbiol-tools.ca/DNA_composition.htm

2. Create Matrix File. Also written by J. Zheng (Queen's University, 
Canada) this program creates a matrix from a DNA Clustal alignment and also 
presents the consensus.  Accessible from: 
http://molbiol-tools.ca/DNA_Motifs.htm this program maybe useful for those 
who want to use:

3. PromScan (D.J. Studholme & R. Dixon. 2003. Domain architectures of 
sigma54-dependent transcriptional activators. J. Bacteriol. 185:1757-67; as 
modified by S. Richards, Queen's University, Canada).  This program scans 
small genomes for potential factor-binding sites including RpoN and 
IHF-binding sites. If a *.ptt file is included the results will indicate 
the position of the promoter relative to the nearest gene.  This is 
accessible from either: http://molbiol-tools.ca/DNA_Motifs.htm or 

4. Java-based programs - in addition to "Molecular Biology Freeware for 
Windows" a new page has been added with Java-based programs 

5. Gester (Genome Scanner for Terminators) - This very useful program for 
predicting transcriptional terminators in DNA sequences (Shyam Unniraman, 
Ranjana Prakash and Valakunja Nagaraja. 2002. Nucleic Acids Research Vol. 
30, No. 3 675-684) is being rendered web available.  When it is ready we 
will make an announcement.


Andrew Kropinski
Andrew M. Kropinski Ph.D.
Professor of Microbiology
Department of Microbiology & Immunology
Queen's University
Kingston, Ontario K7L 3N6

Tel (613) 533-2459
Fax (613) 533-6796
URL http://microimm.queensu.ca/kropinski.htm
Online Analysis Tools: http://molbiol-tools.ca
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