| 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. 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
Chapter 1 images Beyond the book: Finding
out about DNA chips and micro-arrays
Back to Menu
|
| Chapter
2: How Most People Use Bioinformatics
Chapter 2 images The sites everybody should
know about
Back to Menu
|
| Chapter
3: Using DNA databases
Chapter 3 images A few places for finding
genomic information
Back to Menu
|
Chapter
4: Using Protein and Specialized Sequence Databases
Chapter 4 images
The two main information resources about protein sequences
Some good places for refreshing your biochemistry
The main resources for biochemical pathways and enzymes
Some great 3-D structure information resources
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). |
Back to Menu
|
| Chapter
5: Working with a Single DNA Sequence
Chapter 5 images
Some sites for performing DNA analysis
Web Sites for searching motifs in DNA sequences
Back to Menu
|
| Chapter
6 :Working with a Single Protein Sequence
Chapter 6 images
The Main Domain Collections
Protein sequence analysis over the Internet
Back to Menu
|
| Chapter
7: Similarity Searches on Sequence Databases
Chapter 7 images
A few BLAST and PSI-BLAST servers around the world
WU-BLAST
Alternative Methods for Homology Searches
Back to Menu
|
| Chapter
8: Comparing Two Sequences
Chapter 8 images
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
Online pairwise alignment analyses
Back to Menu
|
| Chapter
9: Building a Multiple Sequence Alignment
Chapter 9 images
| 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
A List of ClustalW servers
Multiple Sequence Alignment Resources Over the Internet
Motif-finding methods available online
Back to Menu
|
| Chapter
10: Editing and Publishing Alignments
Chapter 10 images
Packages for Editing Multiple Sequence Alignments
Extracting information from a multiple sequence alignment
Multiple alignment beautifying tools
Back to Menu
|
| Chapter
11: Working with Protein 3-D Structures
Chapter 11 images
Predicting secondary structures
Back to Menu
|
| Chapter
12: Working with RNA
Chapter 12 images
Hunting Micro RNAs (miRNAs) over the Web
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
A list of generic RNA resources
Back to Menu
|
| Chapter
13: Building Phylogenetic Trees
Chapter 13 images
Online sites for making phylogenetic trees
Generic phylogenetic resources on the Internet
Collections of Orthologous Sequences
Back to Menu
|
| Chapter
15: Some Useful Bioinformatics Resources
Ten important bioinformatics databases
Twelve important software programs in bioinformatics
Ten bioinformatics resource locators
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. |
Back to Menu
|
