Unlike DNA replication, transcription results in a RNA complement that substitutes the RNA uracil (U) in all instances where the DNA thymine (T) would have occurred. Both RNA and DNA are nucleic acids, which use base pairs of nucleotides as a complementary language that enzymes can convert back and forth from DNA to RNA. In eukaryotes, this occurs in the nucleus. Bioinformatics, 22:1534-1535).Messenger RNA or mRNA is a type of RNA that is formed by transcription of DNA and encodes a protein.ĭuring transcription, a DNA sequence is copied into a complementary RNA molecule. 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. Similar resources are available here and here. Random DNA sequence generator ( Reference: Villesen, P. Also check out Chapter 5 "Buffer Calculator."ĭSHIFT - a web server for predicting DNA 1H, 13C & 31P chemical shifts ( Reference: S.L. Java based Molecular Biologist's Workbench.Select Chapter 1 for sequence format conversion (upper lower case T U reverse or complement sequence). JaMBW (European Molecular Biology Laboratory of Heidelberg, Germany). Another graphically good site is on the VectorBuilder site. One can click on the peaks and valleys and get a read-out of the localized GC-content. This program was used to generate the following disgram of Escherichia phage lambda (NC_001416) using a window of 48 bp. GC Content Calculator ( Biologics International Corp, Indianapolis, USA ) - DNA GC-content percentage is calculated as Count(G + C)/Count(A + T + G + C) * 100. 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). 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. Genomics %G~C Content Calculator (Science ) - simple calculator for mol%G+C plus counts the individual bases.Ĭompositional heterogeneity: GC Content Plot Online. 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.Ĭompare oligonucleotide frequencies among sequences - This tool will compute distance between input sequences and UPGMA clustering will be display in tabular and dendogram formats. Select "create statistics" and "start task" to get to the sequence entry page. The latter provides a nice output of mono-, di- and trinucleotide frequencies. Well worth running before doing any other analysis.īase composition - consider WORDCOUNT ( EMBOSS Suite) which gives one the option of choosing the "word size". VecScreen (National Center for Biotechnology Information) - screens your DNA sequence for potential vector sequence. A good internet resource on GC content can be found on the website.
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