Bioinformatics For Dummies, 2nd Edition

For your convenience, we have listed the resources chapter by chapter, following the order in which they appear in the book. Along with the chapters the authors have provided images and diagrams used in the book. You may go to the corresponding chapter to download that specific chapter.
(All images are kept in .zip archives and are available on the download tab. You may download winzip a utility to open the archives.)

Chapters:

Chapter 1 Finding Out What Bioinformatics Can Do for You
Chapter 2 How Most People Use Bioinformatics
Chapter 3 Using Nucleotide Sequence Databases
Chapter 4 Using Protein and Specialized Sequence Databases
Chapter 5 Working with a Single DNA Sequence
Chapter 6 Working with a Single Protein Sequence
Chapter 7 Similarity Searches on Sequence Databases
Chapter 8 Comparing Two Sequences
Chapter 9 Building a Multiple Sequence Alignment
Chapter 10 Editing and Publishing Alignments
Chapter 11 Working with Protein 3-D Structures
Chapter 12 Working with RNA Structures
Chapter 13 Building Phylogenetic Trees
Chapter 15 Some Useful Bioinformatics Resources

 

Chapter 1: Finding Out What Bioinformatics Can Do for You

Beyond the book: Finding out about DNA chips and micro-arrays

Address	Description
cmgm.stanford.edu/pbrown/	A leading laboratory offering a complete "do-it-yourself" tutorial on micro-arrays
research.nhgri.nih.gov/microarray/main.html	A great resource from the U.S. National Institutes of Health
www.ebi.ac.uk	The public repository for micro-array data from the European Bioinformatics Institute
www.affymetrix.com	The leading company in DNA chips
www.axon.com	Nice pictures and animations from a leading provider of micro-array readers

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Chapter 2: How Most People Use Bioinformatics

The sites everybody should know about

Address	Description
www.ncbi.nlm.nih.gov/entrez/	The top site for bibliographic information in biomedical sciences
www.expasy.org/sprot/	The best starting point for finding out about proteins and their genes
www.ncbi.nlm.nih.gov	The US site of the joint international DNA sequence repository (GenBank)
www.ebi.ac.uk/embl/	Its counterpart in Europe (EMBL)
www.ddbj.nig.ac.jp	Its counterpart in Japan (DDBJ)
www.ncbi.nlm.nih.gov/BLAST/	The main site to compare your sequence with all others
pir.georgetown.edu	A user-friendly site for analyzing your protein sequence and trying your first multiple sequence alignment with CLUSTALW

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Chapter 3: Using DNA databases

A few places for finding genomic information

Address	Description
www.ncbi.nlm.nih.gov	The US site of the joint international DNA sequence repository (GenBank)
www.tigr.org/tdb/	The Institute of Genomic Research: microbial genomics
www.ensembl.org	The place to find out about the human genome
genome.cse.ucsc.edu	Another user-friendly human genome browser

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Chapter 4: Using Protein and Specialized Sequence Databases

The two main information resources about protein sequences

Address	Description
www.expasy.org/sprot/	The Expasy/SWISS-PROT server
pir.georgetown.edu	The Protein Information Resource server

Some good places for refreshing your biochemistry

Address	Description
www.glycosuite.com	The glycan structure database
lipid.bio.m.u-tokyo.ac.jp	The ultimate lipid database
chem.sis.nlm.nih.gov/chemidplus/	ChemIDplus: Identifying molecules by drawing them up!

The main resources for biochemical pathways and enzymes

Address	Description
www.expasy.ch/cgi-bin/search-biochem-index	Find which metabolic pathway a molecule belongs to.
www.genome.ad.jp/kegg/	The famous Kyoto Encyclopedia of Genes and Genomes (KEGG). E.C. (Enzyme Codes) numbers or gene names are the best starting points for this resource.
brenda.bc.uni-koeln.de	The comprehensive enzyme information system BRENDA.
www.chem.qmul.ac.uk/iubmb	The official site for enzyme nomenclature of the International Union of Biochemistry and Molecular Biology (IUBMB).
www.ecocyc.org	The Encyclopedia of E. coli Genes and Metabolism. It is progressively extending to other bacteria.

Some great 3-D structure information resources

Address	Description
www.rcsb.org/pdb	PDB, the official repository database for protein 3-D structures.
www.ncbi.nlm.nih.gov/Structure	MMDB, NCBI's database of macromolecular 3-D structures with visualization tools.
scop.mrc-lmb.cam.ac.uk/scop	SCOP, a Structural Classification Of Proteins.
www.biochem.ucl.ac.uk/bsm/cath_new	CATH (Class, Architecture, Topology, Homologous superfamily), a hierarchical classification of protein structures.
www.expasy.ch/swissmod/SWISS-MODEL.html	Swiss-Model, a fully automated protein structure homology-modeling server.

Some specialized protein databases

Address	Description
imgt.cines.fr	IMGT, the International Immunogenetics database, specializes in proteins involved in the immune response.
rebase.neb.com	Rebase, the reference restriction-modification enzyme database.
afmb.cnrs-mrs.fr/CAZY	CAZy, an information resource on enzymes that degrade, modify, or create glycosidic bonds.
www.merops.co.uk	MEROPS, a database specializing on proteases.
pkr.sdsc.edu/html/index.shtml	PKR, the Protein Kinase Resource, focuses on the protein kinase family of enzymes.
nrr.georgetown.edu	NRR, the Nuclear Receptor Resource, is a collection of individual databases on the steroid and thyroid hormone receptors.
senselab.med.yale.edu/senselab	The Human Brain Database provides information on the proteins involved in neural processes, such as ion channels, membrane receptors of neurotransmitters and neuromodulators, as well as olfactory receptors (ORDB).
www.ncbi.nlm.nih.gov/COG	The COG (Cluster of Orthologous Groups) database regroups proteins shared by at least three major phylogenetic lineages (ancient conserved domains).

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Chapter 5: Working with a Single DNA Sequence

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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Chapter 6 :Working with a Single Protein Sequence

The Main Domain Collections

PROSITE-Profile (IP)PfamA (IP)PRINTs (IP)PRODOM (IP)SMART (IP)COGs (IP)TIGRFAM (IP)BLOCKs (IP)

Name	Address	Number of Domains	Generation
http://www.expasy.org/prosite	616	Manual
http://www.sanger.ac.uk/Software/Pfam	7973	Manual
http://www.bioinf.man.ac.uk/dbbrosers/PRINTS	1900	Manual
http://protein.toulouse.inra.fr/prodom/current/html/home.php	736000	Manual
http://smart.embl-heidelberg.de	685	Manual
http://www.ncbi.nlm.nih.gov/COG/new/	4852	Manual
http://www.tigr.org/TIGRFAMs	2453	Manual
http://blocks.fhcrc.org	12542	Manual

Protein sequence analysis over the Internet

ExPASyPbilPIRCBSHitsInterProCD search

Name	Site	Description
http://www.expasy.org/tools	Proteins
http://npsa-pbil.ibcp.fr	Proteins
http://pir.georgetown.edu	Proteins
http://www.cbs.dtu.dk/services	Proteins
http://hits.isb-sib.ch/	Proteins
http://www.ebi.ac.uk/interpro/scan.html	Domains
http://www.ebi.ac.uk/InterProScan/	Domains

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Chapter 7: Similarity Searches on Sequence Databases

A few BLAST and PSI-BLAST servers around the world

Country or Continent	Program	URL
USA	BLAST/PSI-BLAST	www.ncbi.nlm.nih.gov/BLAST
Europe	BLAST	www.expasy.ch/tools/blast/
Europe	BLAST	www.ch.embnet.org/software/bBLAST.html
Europe	BLAST	www.ebi.ac.uk/blast
Japan	BLAST/PSI-BLAST	www.ddbj.nig.ac.jp/search/blast-e.html

WU-BLAST

Address	Description
http://blast.wustl.edu/	The Home of WU-BLAST (no online server)
http://tigrblast.tigr.org/tgi//	Program
http://www.genome.wustl.edu/tools/blast/	Program
http://www.ebi.ac.uk/blast/	Program
http://brassica.bbsrc.ac.uk/BrassicaDB/blast_form.html	Program

Alternative Methods for Homology Searches

Country/Continent	Program	Address
USA	FASTA	http://fasta.bioch.Virginia.edu/fasta
EUROPE	FASTA	http://www.ebi.ac.uk/fasta33
EUROPE	SSEARCH	http://www.ch.embnet.org/software/GMFDF_form.html
JAPAN	SSEARCH/FASTA	http://www.ddbj.nig.ac.jp/search/ssearch-e.html
USA	BLAT	http://genome.ucsc.edu

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Chapter 8: Comparing Two Sequences

Various flavors of dot-plot programs

Name	Used For	Range	URL	Platforms
Dotlet	Proteins, DNA	10,000	www.ch.embnet.org	All (Java)
Dnadot	Proteins, DNA	100,000	arbl.cvmbs.colostate.edu/molkit/dnadot/	All (Java)
Dotter	Proteins, DNA	100,000	www.cgr.ki.se/cgr/groups/sonnhammer/Dotter.html	Unix, Linux, Windows
Dottup	Complete genomes, DNA	>100,000	www.emboss.org	Unix, Linux

Online pairwise alignment programs

Name	Address	Alignment Type
lalign	www.ch.embnet.org/software/LALIGN_form.html	Global/Local
lalign	http://fasta.bioch.virginia.edu/fasta_www/plalign.htm	Global/Local
USC	www-hto.usc.edu/software/seqaln/seqaln-query.html	Global/Local
alion	fold.stanford.edu/alion/	Global/Local
align	genome.cs.mtu.edu/align.html	Global/Local
align	www.ebi.ac.uk/emboss/align/	Global/Local
xenAliTwo	www.soe.ucsc.edu/~kent/xenoAli/xenAliTwo.html	Local for DNA
Blast2seqs	www.ncbi.nlm.nih.gov/blast/bl2seq/bl2.html	Local BLAST
Protal2dna	bioweb.pasteur.fr/seqanal/interfaces/protal2dna.html	Protein against DNA
Pal2nal	coot.embl.de/pal2nal	Prottein against DNA

Online pairwise alignment analyses

Name	Address	Function
lalnview	www.expasy.ch/tools/sim-prot.html	Visualization
prss	www.ch.embnet.org/software/PRSS_form.html	Evaluation
prss	fasta.bioch.virginia.edu/fasta/prss.htm	Evaluation
graph-align	darwin.nmsu.edu/cgi-bin/graph_align.cgi	Evaluation

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Chapter 9: Building a Multiple Sequence Alignment

Application	Procedure
Extrapolation	A good multiple alignment can help convince you that an uncharacterized sequence is really a member of a protein family. Alignments that include SWISS-PROT sequences are the most informative. Use the ExPASyBLAST server (at www.expasy.ch/tools/blast/) to gather and align them.
Phylogenetic analysis	If you carefully choose the sequences you include in your multiple alignment, you can reconstruct the history of these proteins. Use the Pasteur Phylip server at bioweb.pasteur.fr/seqanal/phylogeny/phylip-uk.html.
Pattern identification	By discovering very conserved positions, you can identify a region that is characteristic of a function (in proteins or in nucleic-acid sequences). Use the logo server for that purpose: www-lmmb.ncifcrf.gov/~toms/sequencelogo.html.
Domain identification	It is possible to turn a multiple sequence alignment into a profile that describes a protein family or a protein domain (PSSM). You can use this profile to scan databases for new members of the family. Use NCBI-BLAST to produce and analyze PSSMs: www.ncbi.nlm.nih.gov/blast/blastcgihelp.shtml#pssm.
DNA regulatory elements	You can turn a DNA multiple alignment of a binding site into a weight matrix and scan other DNA sequences for potentially similar binding sites. Use the Gibbs sampler to identify these sites: bayesweb.wadsworth.org/gibbs/gibbs.html
Structure prediction	A good multiple alignment can give you an almost perfect prediction of your protein secondary structure for both proteins and RNA. Sometimes it can also help in the building of a 3-D model.
nsSNP analysis	Various gene alleles often have different amino-acid sequences. Multiple alignments can help you predict whether a Non-Synonymous Single-Nucleotide Polymorphism is likely to be harmful. See the SIFT site for more details: blocks.fhcrc.org/sift/SIFT.html.
PCR Analysis	A good multiple alignment can help you identify the less-degenerated portions of a protein family, in order to fish out new members by PCR (polymerase chain reaction). If this is what you want to do, you can use the following site: blocks.fhcrc.org/codehop.html.

BLAST servers integrating multiple alignment methods

Address	What You Can Do There
www.expasy.ch/tools/blast/	Extract entire sequences, Export sequences in FASTA, Submit sequences to ClustalW, Tcoffee or MAFFT. Turn the list of Hits into a non-redundant collection of sequences
npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_blast.html	Extract entire sequences; Extract sequence fragments; Export sequences in FASTA; Submit sequences to ClustalW
srs.ebi.ac.uk	Submit sequences to ClustalW

A List of ClustalW servers

Name	Location	URL
EBI	Europe	www.ebi.ac.uk/clustalw
EMBnet	Europe	www.ch.embnet.org/software/ClustalW.html
PIR	USA	pir.georgetown.edu/pirwww/search/multaln.html
BCM	USA	searchlauncher.bcm.tmc.edu/multi-align/multi-align.html
GenomeNet	Japan	align.genome.jp/
DDBJ	Japan	www.ddbj.nig.ac.jp/search/clustalw-e.html
Strasbourg	Europe	ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalW/

Multiple Sequence Alignment Resources Over the Internet

Method	Description	Address
Tcoffee	Accurate combination of sequences and structures	www.tcoffee.org www.ch.embnet.org/software/TCoffee.html www.ebi.ac.uk/t-coffee/
Probcons	A Bayesian version of Tcoffee	probcons.stanford.edu/
MUSCLE	A fast and accurate sequence cruncher	www.drive5.com/muscle/
Kalign	A fast sequence aligner	msa.cgb.ki.se
MAFFT	A fast and accurate sequence cruncher using Fast Fourier Tranforms	timpani.genome.ad.jp/~mafft/server/
Dialign	Ideal for Sequences With Local Homology	bibiserv.techfak.uni-bielefeld.de/dialign/

Motif-finding methods available online

Method	Address
Gibbs Sampler	bioweb.pasteur.fr/seqanal/interfaces/gibbs-simple.html bayesweb.wadsworth.org/gibbs/gibbs.html
Pratt	www.ebi.ac.uk/pratt/index.html
eMotif	dna.stanford.edu/emotif/
MEME	meme.sdsc.edu/meme/
TEIRESIAS	cbcsrv.watson.ibm.com/Tspd.html
Bioprospector	ai.stanford.edu/~xsliu/BioProspector/
Improbizer	www.soe.ucsc.edu/~kent/improbizer/improbizer.html
BLOCK-Maker	blocks.fhcrc.org/blocks/blockmkr/make_blocks.html

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Chapter 10: Editing and Publishing Alignments

Packages for Editing Multiple Sequence Alignments

Name	Address	Description
Jalview	www.jalview.org www.es.embnet.org/Services/MolBio/jalview/	Java package, available online
Kalignview	msa.cgb.ki.se	Nice online alignment viewer
CINEMA	www.bioinf.man.ac.uk/dbbrowser/CINEMA2.1/	A very complete Java package
Seaview	pbil.univ-lyon1.fr/software/seaview.html	A beautiful editor, very easy to install
Belvu	www.cgr.ki.se/cgr/groups/sonnhammer/Belvu.html	Useful for removing redundancy
Bioedit	www.mbio.ncsu.edu/BioEdit/bioedit.html	Adapted for RNA
RALEE	www.sanger.ac.uk/Users/sgj/ralee/	An RNA viewer
Review	bioweb.pasteur.fr/cgi-bin/seqanal/review-edital.pl	A very complete list of viewers

Extracting information from a multiple sequence alignment

in your multiple alignment

Name	URL	Description
Logo	weblogo.berkeley.edu , www-lmmb.ncifcrf.gov/~toms/sequencelogo.html, www.cbs.dtu.dk/~gorodkin/appl/plogo.html	Logos
Blocks	blocks.fhcrc.org/blocks/process_blocks.html	Identifies blocks
Blockgap	www.bork.embl-heidelberg.de/Alignment/blockgap.html
Lama	blocks.fhcrc.org/blocks-bin/LAMA_search.sh	Compares your multiple alignment with the BLOCKs database
Amas	www.compbio.dundee.ac.uk/servers/amas_server.html	Identifies important features in the multiple alignment

Multiple alignment beautifying tools

Name	URL	Description
ESPript	espript.ibcp.fr	A very powerful shading-and-coloring tool
Boxshade	www.ch.embnet.org/software/BOX_form.html	Shading in black and white
Mview	bioweb.pasteur.fr/seqanal/interfaces/mview_blast-simple.html	Can process BLAST alignments

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Chapter 11: Working with Protein 3-D Structures

Predicting secondary structures

URL	Description
bioinf.cs.ucl.ac.uk/psipred/	PsiPred for predicting protein secondary structures
cubic.bioc.columbia.edu/predictprotein www.embl-heidelberg.de/predictprotein www.cmbi.kun.nl/bioinf/predictprotein www.sdsc.edu/predictprotein	PredictProtein for predicting protein secondary structures
www.rcsb.org/pdb/	The Protein Database, containing every publicly available protein structure
www.ncbi.nlm.nih.gov/Structure	The NCBI section dedicated to structure analysis
www.rasmol.org www.expasy.ch/swissmod/SWISS-MODEL.html	Two very popular PDB viewers (you must install them on your machine)
www.biochem.ucl.ac.uk/bsm/cath_new/ www2.ebi.ac.uk/dali/ scop.mrc-lmb.cam.ac.uk/scop	Popular structure classification collections
guitar.rockefeller.edu/modeller/modeller.html www.expasy.ch/swissmod/SWISS-MODEL.html	Homology modeling
www.ncbi.nlm.nih.gov/Structure/RESEARCH/threading.html compbio.ornl.gov/structure/prospect	Threading sequences onto PDB structures
folding.stanford.edu	ab-initio folding
www.scripps.edu/brooks molmovdb.mbb.yale.edu/	MolMovDB Molecular dynamics
www.bio.vu.nl/nvtb/Docking.html	Protein Interaction

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Chapter 12: Working with RNA

Hunting Micro RNAs (miRNAs) over the Web

Address	Description
sirna.cgb.ki.se/	An extensive collection of resources on silencing RNAs
itb.biologie.hu-berlin.de/~nebulus/sirna/v2/	A database of all known human silencing RNAs
microrna.sanger.ac.uk/sequences	The home of miRNAs at the Sanger Center in the UK. Probably one of the most extensive resources on micro-RNAs.
cbit.snu.ac.kr/~ProMiR2/	A resource for predicting miRNAs using probabilistic methods.
pictar.bio.nyu.edu/	Prediction of the potential target of your miRNA on complete genomes.
bibiserv.techfak.uni-bielefeld.de/rnahybrid/	A resource for predicting the potential target of your miRNA on a user-provided genomic sequence.
mirna.imbb.forth.gr/microinspector/	Runs your genomic sequence against an exhaustive database of miRNAs

Ribosomal RNA resources on the Internet

URL	Description
www.psb.ugent.be/rRNA/lsu/	A European database on the larger of the two ribosomal subunits. It contains predicted structures. It is possible to query the database online. Features lots of online software.
www.psb.ugent.be/rRNA/ssu/	The "other" European database, this time dedicated to the small ribosomal subunit.

Some non-coding RNA resources

URL	Description
condor.bcm.tmc.edu/smallRNA/smallrna.html	Dedicated to small non-coding RNAs.
rna.wustl.edu/tRNAdb/	Dedicated to tRNAs.
bighost.area.ba.cnr.it/BIG/UTRHome/	Dedicated to the untranslated regions of genes.
www.indiana.edu/~tmrna/	Dedicated to the recently discovered tmRNA that are both transfer and messenger RNAs. (If you don't yet know what this is, you MUST take a look at this fascinating Web site!)

A list of generic RNA resources

URL	Description
bioinfo.lifl.fr/rna/	A site dedicated to the detection of non-coding RNAs.
www.imb-jena.de/RNA.html/	RNA World, one of the most complete sites currently available.
www.rnabase.org/links/	Another very complete list of sites.

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Chapter 13: Building Phylogenetic Trees

Online sites for making phylogenetic trees

Address	Description
www.ebi.ac.uk/clustalw/	You can use ClustalW to build multiple alignments and compute NJ trees. Remember: You cannot do both at the same time!
www.genebee.msu.ru/clustal/basic.html	The Genebee server can produce genuine phylogenetic trees in one step.
www.tcoffee.org	Tcoffee computes a genuine NJ-phylogenetic tree in one step
www.jalview.org	You can use Jalview to produce NJ trees. Its a very powerful tool that combines alignment editing with tree computation.
atgc.lirmm.fr/phyml/	A powerful method to compute maximum likelihood trees from Gascuel and his team.
bioweb.pasteur.fr/seqanal/interfaces/bionj-simple.html	An interface to BioNJ, a novel NJ method.
www.up.univ-mrs.fr/evol/figenix/	A powerful Java tool to gather members of a protein family and build the associated tree.
bioweb.pasteur.fr/seqanal/phylogeny/phylip-uk.html	A Web interface for Phylip.
www.genebee.msu.ru/services/phtree_reduced.html	Very powerful interface for a new tree reconstruction method.

Generic phylogenetic resources on the Internet

Address	Description
evolution.genetics.washington.edu/phylip/software.html	Joe Felsenstein's pages, where Phylip lives; it's also one of the most extensive collections of resources available. Truly a legendary site!
www.ucmp.berkeley.edu/subway/phylo/phylosoft.html	A very complete list of phylogeny resources.
paup.csit.fsu.edu/index.html	The home of PAUP, legendary phylogeny package using Parsimony. Although PAUP is a commercial package, its reasonably priced and worth every penny, according to specialists.
www.ncbi.nlm.nih.gov/About/primer/phylo.html	The NCBI primer on phylogeny.
www.techfak.uni-bielefeld.de/bcd/Curric/MathAn/mathan.html	A high-quality course on tree reconstruction methods.

Collections of Orthologous Sequences

Address	Description
www.ncbi.nlm.nih.gov/COG/	Clusters of orthologous sequences maintained by the NCBI. Each cluster contains proteins from bacterial genomes.
pbil.univ-lyon1.fr/databases/hovergen.html	A collection of orthologous vertebrate genes.
pbil.univ-lyon1.fr/databases/hobacgen.html	A collection of orthologous bacterial genes.
systers.molgen.mpg.de	Another collection of homologous sequences.
rdp.cme.msu.edu, www.psb.ugent.be/rRNA/ssu/, www.psb.ugent.be/rRNA/lsu/	Three extensive collections of ribosomal RNA sequences, which are very useful for classifying new organisms, and come with appropriate phylogenetic tools.

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Chapter 15: Some Useful Bioinformatics Resources

Ten important bioinformatics databases

Name	URL	Description
GenBank/DDBJ/EMBL	http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Nucleotide	Nucleotide sequences
Ensembl	www.ensembl.org	Human/mouse genome
PubMed	http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed	Literature references
NR	http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Protein	Non redundant Protein sequences
SWISS-PROT	www.expasy.ch	Protein sequences
InterPro	www.ebi.ac.uk	Protein domains
OMIM	www.ncbi.nlm.nih.gov	Genetic diseases
Enzymes	www.chem.qmul.ac.uk	Enzymes
PDB	www.rcsb.org/pdb/	Protein structures
KEGG	www.genome.ad.jp	Metabolic pathways

Twelve important software programs in bioinformatics

Category	Name	URL	Description
Database Search	SRS	srs.ebi.ac.uk	Database search
	Entrez	www.ncbi.nih.gov/Entrez	Database search (Chapter 3)
	BLAST	www.ncbi.nlm.nih.gov/blast	Homology search (Chapter 7)
	DALI	www.ebi.ac.uk/dali	Structure database search (Chapter 11)
Multiple alignment	ClustalW	www.ebi.ac.uk	Multiple sequence alignment (Chapter 9)
	MUSCLE	phylogenomics.berkeley.edu/muscle/	Multiple sequence alignment (Chapter 9)
	Tcoffee	www.tcoffee.org	Multiple Sequence Alignment (Chapter 9)
Prediction	GenScan	genes.mit.edu	Gene prediction (Chapter 5)
	PsiPred	bioinf.cs.ucl.ac.uk/psipred/	Protein structure prediction (Chapter 11)
	Mfold	www.bioinfo.rpi.edu/applications/mfold/	RNA structure prediction (Chapter 12)
Phylogenetics	Phylip	bioweb.pasteur.fr/seqanal/phylogeny/phylip-uk.html	Tree reconstruction (Chapter 13)
	PhyML	atgc.lirmm.fr/phyml/	Tree reconstruction (Chapter 13)
Edition/Visualization	Jalview	www.jalview.org	Alignment editor (Chapter 10)
	Logos	weblogo.berkeley.edu	A MSA Visualization Tool (Chapter 10).
	Trees	iubio.bio.indiana.edu/treeapp/treeprint-form.html	Tree Visualization (Chapter 13).
	Rasmol	www.umass.edu/microbio/rasmol/	Structure visualization (Chapter 11)

Ten bioinformatics resource locators

Name	Address	Description
ExPASy	www.expasy.ch	Dedicated to proteins
ArrayExpress	www.ebi.ac.uk/microarray/	DNA chips
Swbic	www.swbic.org	Miscellaneous links
Pasteur	bioweb.pasteur.fr/intro-uk.html	Miscellaneous links; many online tools
RNA World	www.imb-jena.de/RNA.html	RNA-related links
miRNAs	microrna.sanger.ac.uk/sequences/index.shtml	Extensive Resources on miRNA
Phylip	evolution.genetics.washington.edu/phylip/software.html	Everything on phylogeny
NCBI primers	www.ncbi.nlm.nih.gov/education	Very good primers on many subjects
Bielefeld	bibiserv.techfak.uni-bielefeld.de/intro/dist.html	Awesome online course
Bio-informer	www.ebi.ac.uk/Information/News/	The EBI online news
Coffee Corner	www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowSection&rid=coffeebrk	NCBI Online News.

Ten Places to Go Farther

Name	Address	Description
Nucleic Acid Research	nar.oxfordjournals.org/	Once a year, NAR publishes both a database issue and Web-server issue. These are available for free -- and contain the state of the art in bioinformatics.
Nucleic Acid Research	bioinformatics.oxfordjournals.org/	Bioinformatics contains articles describing the most recent methods in bioinformatics.
Nucleic Acid Research	www.iscb.org/events/event_board.php	An exhaustive list of major conferences in the field of bioinformatics, provided by the International Society For Computational Biology.

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