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

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

Base composition - consider WORDCOUNT (Pasteur Institute, France) which gives one the option of choosing the "word size", and GEMS (Genomatix, Germany).  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.

Compositional heterogeneity - Graphe:ADN riche en: (Atelier BioInformatique l'Université de Provence, France) N.B. In French but obvious (Soumettre = Submit). Presents in graphic format AT, GC or single base enrichment in the sequence.
Graph DNA: 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. Alternative locations for cumulative GC skew are the GC  Skew Tool (University of Pittsburgh, U.S.A.), and GenSkew (Munich Information Center for Protein Sequences, Germany). In the first two cases one can only analyze ca. 30 kb of DNA sequence.

Z curve (Centre of BioInformatics,Tianjin University, China) - results in unique three-dimensional curve representations for a given DNA sequence, which is composed of three components ( xn, yn and zn):

• the x-component of a Z curve xn displays the distribution of purine/pyrimidine (R/Y) bases along the sequence;

• the y-component of a Z curve yn displays the distribution of amino/keto (M/K) bases along the sequence;

• the z-component of a Z curve zn displays the distribution of strong-H bond/weak-H bond (S/W) bases along the sequence

DNA base composition analysis tool  (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. 

Sequencing Shuffling - (Arizona Research Labs) In some cases (BLAST, M-Fold) one might want a randomized sequence to compare with one's own.

 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."  Another site offering a variety of output styles (MSF, Phylip, Fasta, GCG etc.) is ReadSeq (Pasteur Institute, France).  N.B. this serves as a complement to the former site.

 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)

 Computation of size of DNA and Protein Fragments from Their Electrophoretic Mobility (Reference: Raghava, G. P. S. 2001. Biotech Software and Internet Report 2:198-200).