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
http://molbiol-tools.ca/Promoters.htm.
4. Java-based programs - in addition to "Molecular Biology Freeware for
Windows" a new page has been added with Java-based programs
(http://molbiol-tools.ca/Java.htm).
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.
Regards
Andrew Kropinski
Andrew M. Kropinski Ph.D.
Professor of Microbiology
Department of Microbiology & Immunology
Queen's University
Kingston, Ontario K7L 3N6
Canada
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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