COMPOSITION

IUB (Degenerate Bases) Code Table

IUB Code

N

V

B

H

D

K

S

W

M

Y

R

Bases

A,C,G,T

G,A,C

G,T,C

A,T,C

G,A,T

G,T

G,C

A,T

A,C

C,T

A,G

A good internet resource on GC content can be found on the bionity.com website.

red_bullet.gif (914 bytes) VecScreen (National Center for Biotechnology Information) - screens your DNA sequence for potential vector sequence.  Well worth running before doing any other analysis.

red_bullet.gif (914 bytes) Base composition - consider WORDCOUNT  (EMBOSS Suite) which gives one the option of choosing the "word size".  The latter provides a nice output of mono-, di- and trinucleotide frequencies. Select "create statistics" and "start task" to get to the sequence entry page.

red_bullet.gif (914 bytes) Oligonucleotide frequencies calculator - in addition to calculating the number and frequency of monomeric to octomeric sequences this site also will calculate Zero Order Markov chain for tetranucleotides (ZOM);  First Order Markov chain for tetranucleotides (FOM); Second Order Markov chain for tetranucleotides (SOM); and, Z-scores for tetranucleotides.

red_bullet.gif (914 bytes) Compare oligonucleotide frequencies among sequences - This tool will compute distance between input sequences and UPGMA clustering will be display in tabular and dendogram formats.

red_bullet.gif (914 bytes) Genomics %G~C Content Calculator (Science Buddies.org) - simple calculator for mol%G+C plus counts the individual bases. 

red_bullet.gif (914 bytes) Compositional heterogeneity: GC Content Plot Online.

red_bullet.gif (914 bytes) GraphDNA - DNA Skew Graphing (Viral Bioinformatics Resource Center, University of Victoria, Canada) - this Java applet performs DNA walks, purine, AT and GC skews on small (<1 Mb) genomes. Requires registration and login. Alternative locations for cumulative GC skew are the GC  Skewing (Davidson College, U.S.A.), and GenSkew: Genomic nucleotide skew application (Developed by TU Munich; maintained by Department of Computational Systems Biology of the University of Vienna, Austria) . 

red_bullet.gif (914 bytes) GC Content Calculator  (Biologics International Corp, Indianapolis, USA)  - DNA GC-content percentage is calculated as Count(G + C)/Count(A + T + G + C) * 100. This program was used to generate the following disgram of Escherichia phage lambda (NC_001416) using a window of 48 bp. One can click on the peaks and valleys and get a read-out of the localized GC-content.  Another graphically good site is on the VectorBuilder site.

red_bullet.gif (914 bytes) JaMBW (European Molecular Biology Laboratory of Heidelberg, Germany). Java based Molecular Biologist's Workbench.Select Chapter 1 for sequence format conversion (upper lower case; T  U; reverse or complement sequence).  N.B. Also check out   Chapter 5 "Buffer Calculator."  

red_bullet.gif (914 bytes) DSHIFT - a web server for predicting DNA 1H, 13C & 31P chemical shifts (Reference: S.L. Lam. 2007. Nucl. Acids Res. 35(Web Server issue): W713-W717)

red_bullet.gif (914 bytes) Random DNA sequence generator (Reference: Villesen, P. 2007.  Molecular Ecology Notes 7: 965–968.).  Similar resources are available here and here.
red_bullet.gif (914 bytes) GenRGenS, a software dedicated to random generation of genomics sequences that supports several classes of models, including Markov chains, HMM, context-freegrammars, PROSITE patterns and more. (Reference: Y. Ponty et al. Bioinformatics, 22:1534-1535).