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For Dummies® Bonus Material
By: Jean-Michel Claverie Ph.D., Cedric Notredame Ph.D.

[Bio FD Home][Ch.1][Ch.2][Ch.3][Ch.4][Ch.5][Ch.6][Ch.7][Ch.8][Ch.9][Ch.10][Ch.11][Ch.12][Ch.13][Ch.15]

Chapter 5: Working with a Single DNA Sequence

Chapter 5 images

Some sites for performing DNA analysis

Address	Description
VecScreen_docs	Screen your sequence for vector contamination
repeatmasker.genome.washington.edu	Tools for detecting and masking repeats
www.firstmarket.com/cutter/cut2.html biotools.umassmed.edu/bioapps/rsites.html rebase.neb.com	Sites to compute restriction maps for your sequence
biotools.umassmed.edu	Designing PCR primers
bioweb.pasteur.fr	Tools for various DNA composition analyses
arbl.cvmbs.colostate.edu/molkit/ www.ch.embnet.org	Two sites for interactive dot-plot analysis
www.ncbi.nlm.nih.gov/gorf/gorf.html	A basic ORF finder
opal.biology.gatech.edu/GeneMark www2.ebi.ac.uk/genemark/	Gene prediction in prokaryotes using GeneMark
argon.cshl.org/genefinder/ corba.ebi.ac.uk/cgi-bin/sp/wrapper.cgi genome.cs.mtu.edu/aat/aat.html	Various sites for predicting protein-coding genes in eukaryote DNA sequences
genes.mit.edu/genomescan	For predicting complete gene structures from vertebrate DNA sequences
bio.ifom-firc.it/ASSEMBLY/assemble.html	A straightforward Web-service for small-scale gene assembly
www.mrc-lmb.cam.ac.uk/pubseq/staden_home.html www.phrap.org www.tigr.org/software www.acedb.org	Popular software for assembling and managing DNA sequences (you need to install them on your computer)
www.genecodes.com www.dnastar.com www.paracel.com	Main commercial sequence assembly software

Web Sites for searching motifs in DNA sequences

Address	Description
transfac.gbf.de/TRANSFAC/	Search for potential transcriptional elements using the TRANSFAC database
bimas.dcrt.nih.gov/molbio/matrixs/	Search for transcriptional elements using the IMD database
bimas.dcrt.nih.gov/molbio/proscan/	Predict putative eukaryotic promoter regions
www.gsf.de/biodv/genomeinspector.html	Detect distance correlations between sequence elements
www.dna.affrc.go.jp/htdocs/PLACE/signalscan.html	Detect regulatory signals in plant sequences
meme.sdsc.edu/meme/website/	Discover motifs in groups of related DNA or protein sequences
rsat.ulb.ac.be/rsat/	Tools to analyze regulatory sequences


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