Introduction to Genome Bioinformatics, PLPTH
890
CN's
bioinformatics & other WWW links
Dead links removed 12/21/04.
New resources not yet integrated 12/04
Table
of contents
Uses GCG
Uses
MacVector
Bioinformatics
Sequence search sites
- NCBI
HomePage
- Entrez Home
- BLAST
@ NCBI
- PSI-BLAST @ NCBI
- NCBI dbEST
- BLAST Archive at Washington
University, St. Louis
- FASTA
@ EBI
- Bioccelerator
@ EMBL
- ITEC BLAST Search
- ParAlign
and Smith-Waterman - Rapid and sensi...
- PowerBlast
- FASTA at University of Virginia
- MuSeqBox
Online
Tutorials/lectures
Protein
pattern searching
- Protein Pattern, Motif, and Domain Databases
Weight matrices
- Weight Matrices for
Sequence Similarity Scoring
Gene-finding
- Computational Gene Identification
General
bioinfo/seq anal
- Brown_NYU course, Using Computers in MB
- BioComputing Hypertext
Coursebook
- IMB Jena Global Library - Biology: Tutorial,
Books Miscellaneous
- SDSC Biology Workbench
- VSNS Biocomputing
Division
Unix
- UNIX
Tutorial for Beginners
- Book I. Basic Introduction
(including email)
- UNIXhelp for users
- PSC Unix tutorial
- UnixWorld Online: Tutorial Article: No.
018 -...
- R2
org uk UNIX Shell Tutorial
- Unix commands
- Unix
Station--Welcome
- ISU Unix tutorial
EMACS
- emacs.pdf
WWW
& network stuff
- NCSA--A Beginner's Guide to HTML Home Page
- HTML guide, Raggett
- GNA-VSNS Biocomputing
Course Chapter 2
- Using FTP; PSC tutorial
Hidden
Markov
- HMM tutorial/Karchin
- ISMB99 Making the most of your HMMs
Sequence
comparison
Tutorial pages
- PSC bioinfo tutorials
- BIOINFORMATICS PRACTICAL
Protein
structure/homology modeling
- Homology
modelling for beginners
- Formalising protein topology TOPS
- A
Guide to Structure Prediction
Database
theory/design/querying
- Intro to database
modeling in bioinfo
- SQL
Tutorial
Perl
- Perl Programming Course for Bioinformatics
an...
- bioperl
course
3D
structure viewing
- CMU RasMol Tutorial
- Resource-list
pages
Lists
of tutorials (out of date)
- Tutorials and Lecture Notes on Bioinformatics
Lists of bioinformatics
sites
- Databases
and Search Tools
- GenomeWeb
Lists
of EVERYTHING bioinformatical
- The
Bioinformatics Resource at the HGMP-RC
- Amos'
links
Lists
of training programs
- Home Pages for Other Bioinformatics Courses
Tool-center
pages
- SDSC
Biology Workbench
- ExPASy
Proteomics tools
- NAR database list
- BCM Search Launcher
- Atelier Bioinformatique
- Biology
Student Workbench
- SRS6
Microarrays
- Alan Robinson
Web Page - Visualisation, Data Mining and Bioinformatics
- Laboratory
for the analysis of microarray data: Main page
- Welcome
to Speed's Microarray Homepage
- DNA Microarrrays
- Microarray
Pages
- microarrays.org
- protocols
- MIR/Gene Expression
- YFLeung's
microarray site
SNPs
Genome-scale
analysis (change name...)
- Microbial Genome Database for Comparative Analysis
- COGs (Clusters of Orthologous Groups of proteins)
- STRING (Search Tool for the Retrieval of Interacting Genes and Proteins)
Gene
regulation
- TRANSFAC
- EPD (Eukaryotic Promoter Database)
- SCPD (S. cerevisiae Promoter Database)
- DPInteract
- AlignACE
Homepage
Transmembrane
helix prediction
- TMHMM
- SOSUI
- TMpred
Extracting
motifs, profiles, hidden-Markov models
- DEAMBULUM
: Search for a pattern
- Hidden
Markov Model (HMM) Toolbox for MATLAB
- Gibbs Motif Sampler
- MEME
- SAM (Sequence Alignment and Modeling system)
- Pratt -- a pattern discovery tool
- Block Maker Help
Spectral analysis of
sequence
- Structural analysis of DNA sequence
- The Autocorrelation function and Periodicity
Protein
domain searches
- MOTIF:
Searching Protein and Nucleic Acid Sequence Motifs
- PROSITE
- InterPro
- SMART
- Pfam
- PFAM
- ProDom
- PRINTS Database
- Blocks
- Protein Domain Profile Analysis @ BMERC
- TIGRFAMs
- Protein Family Databases
- ISREC ProfileScan Server
3D
molecular structure resources
- 3D-PSSM
Protein Fold Recognition (Threading) Server
- PDB
- RasMol/Protein
Explorer
- SCOP
- UCL
BSM CATH classification
- The
DALI Domain Database
- FSSP
- SWISS-MODEL, an Automated Comparative Protein Modelling Server
- Structure
Prediction Meta-server
- DALI
- DSSP, Definition of Secondary Structure of Proteins from 3D coordinates
- HSSP
Database, homology-derived secondary structure of proteins
- PredictProtein & PHD
Data
pipelines
- PEDANT, Protein Extraction, Description and ANalysis Tool
- OSU Bioinformatics
Laboratory
Metabolic
pathway analysis
- The Seed: an Annotation/Analysis Tool
- Puma2: high-throughput comparative analysis of genomes & metabolic networks
Metabolic,
gene-regulatory & signal-transduction-network databases
- KEGG
- stke, Signal Transduction Knowledge Environment
- EcoCyc
- SPAD, Signaling Pathway Database
- DIP, Database of Interacting Proteins
- aMAZE
- Repeatmasker
- UTR-extender, mRNA Extension using Genomic EST Alignments
- CpG
Islands
- NetStart, neural network predictions of translation start sites
- ATGpr, identifying initiation codons in DNA sequences
- SignalP, prediction of signal peptide cleavage sites
- PSORT, prediction of protein localization sites in cells
- CBS
Prediction Servers
Human
genome browsing
- Human
Genome Browser
- NHGRI Online Research Resources
- Ensembl
Genome Browser
Demo
WWW pages
Dynamic
programming
- Modern
algebra visualization
- Math
& physics visualization
Bioinformatics
courses
General
Uses
GCG
- Sequence alignment exercises, PSC
- MB&B 452a/752a12 (Genomics and Bioinformatics), 2003
- Biochem508 (Computer Analysis of DNA and
Protein Sequences), 2004
- Bio520 (Bioinformatics), 2004 & earlier
- 410.633.71 (Computing in Molecular Biology),
1999
- Pharm207/Bio207 (Using Internet Resources
in Molecular Biology), 2003
- MOLB 470 Bioinformatics and Genome Analysis
- Spring 2001
- MOLB 470 table of
contents
- MOLB 470 Schedule
- NMSU MOLB 550 syllabus Spring 1998
Computational
biology/genomics
Bio5495/BME537 (Computational Molecular
Biology), 2004
CSE590CB (Reading and Research in Computational
Biology), 2000
CSE527 - formerly CSE590BI (Computational
Biology), 2000
UCSC BME 100 Fall 2001
Biochemistry218/MIS231 (Computational Molecular
Biology), Stanford
Biochemistry118Q (Genomics and Bioinformatics),
1999
MIS214/CS274 (Representations and Algorithms
for Computational Molecular Biology), 2004
CS690B (Topics in Bio-Informatics), Purdue, 1998
G63.2856/G22.3033 (Computational Genomics),
1999
18.417 (Introduction to Computational Molecular
Biology), 1998
CS600.439 (Computational Biology), 1999,
1996
410.639.71 (Protein Bioinformatics), Johns Hopkins, 2004
CMP243 (Bioinformatics), 1998
Gen/ComS 596X schedule (Genomic data processing)
Washington U. StL course, Computational Molecular
Biology, 2004
Biophysics101: Lecture Notes, Harvard, 2003
Chemistry 160/260: Bioinformatics and Genomics, UCLA 2002
Uses MacVector
- Bio03-510 (Computational Biology), Carnegie Mellon, 2004
- Bio03-311 (Introduction to Computational
Molecular Biology), 2004
- Bio03-310 (Introduction to Computational
Biology), 2004
Protein
structure
- Biochem 503, U. Virginia 2004
Bioinformatics
curricula & faculties
- Graduate
Studies in Computational Molecular Biology, Rutgers
- Penn Center for Bioinformatics, U Pennsylvania
- Summer Institute in Statistical Genetics, NCSU, 2004
- Bioinformatics:
Academic/Degree Programs
Bioinformatics software
Microarray
analysis
- ARGUS microarray data analysis
- MAExplorer
Sequence
processing
- PHRED base-calling software
- Convert Sequence Formats using ReadSeq
- Translate
Tool at ExPASy
- Reverse complement nucleotide sequences
- Melting: enthalpy, entropy, and melting temperature calculation
- Webcutter: find restriction sites in a DNA sequence
- PrimerDesign;
Becker/Marburg
Genomic
sequence viewers
- The GESTALT Workbench
- NHGRI: WebBLAST HomePage
Gene
prediction
- Genscan
- Genie
- GLIMMER: finding genes in microbial DNA
- tRNAscan - SE 1.1
- GFF (General Feature Format) Specification
- PROCRUSTES: Similarity-Based Gene Recognition
via Spliced Alignment
- GeneMine: Free at
last!
- BDGP:
Splice Site Prediction by Neural Network
- GeneBuilder:
CNR gene structure prediction
- WebGene Home
Page
Sequence-alignment
visualization
- USC Sequence Alignment Server
- T-COFFEE
- ClustalW
@ EBI
- BOXSHADE: printouts from multiple-aligned protein or DNA sequence
- SIM4: for aligning cDNAs with genomic sequence
- Wise2: compare a protein sequence to a genomic DNA sequence
- PipMaker: makes percent identity plots of similar regions in two DNA sequences
- VISTA tools for comparative genomics
- JalView
- Java alignment editor
- GeneDoc Multiple Sequence Alignment Editor
- PRSS Server: evaluates the significance of a protein sequence alignment
- LALIGN Local Alignments
- SIM alignment tool for protein sequences
- CINEMA Color INteractive Editor for Multiple Alignments
Dot
plots
- About Dotlet
- Dotter
DNA marker/QT analysis
- QTL Express
- MDM
- PLABSTAT and PLABQTL Software
Tandem-repeat
finding
- Tandem
Repeats Finder
Commercial
- Visualize Inc.
- LabBook
- MDL Information Systems - Downloads
- Lasergene Demo Request Form
Software
resource lists
- EBI Biocatalog
Relationship
visualization
- PhyloGrapher
Welcome
- Species
2000
- PHYLIP
- TreeView tree-drawing softwar
Bioinformatics
programming
- The Bioinformatics Template Library (BTL)
- EMBOSS Homepage
Definitions/overviews
- What is Bioinformatics? (Georgia Tech)
Exercises for CN class
- Fast Database Searches
exercises
- www.techfak.u...uestion3.html
- Alignment of UspA's and MJ0577 relatives
- Bioinfo tutorial, CELL BIOLOGY 220 JMU
- Molecular
biology educational package
- RECOMB 2000 List of accepted posters
- NCBI Problem Set
- Biochem508 - Sequence exercises II
- Multiple Alignment Exercises
- Pathobiology8-140 (Protein Sequence Analysis),
1999
Course exams & problems
- UAriz MCB 416/516
exam
- Final Projects for
Biochem 218/ MIS 231
- Assign3FlowChart.gif 750x925 pixels
Phylogenetic
tree building
- Generating a phylo. tree from MSA
Readings
for CN class
What
is bioinformatics
<>www.oreilly.com --Computers
+ Biology = Bioinformatics
- PatSearch paper
in Bioinformatics
Perl
in bioinformatics
- Stein article on sequence process pathway
- In
Silico Biology - Articles
Literature
- Medline / PubMed
Useful references
- Bioch508 -- Sequence Alignment
Bioinfo groups
& centers
Lloyd
Allison
- Bioinformatics, Computational
Molecular Biology - Alignment, Strings, Sequences, Trees, Maps
- Reconstruction of Strings Past
- Hidden Markov Models
- Hui-Hsien
Chou's Home Page
- Stein
Laboratory
- Institute for Genomic Diversity Home Page
- National Center for Genome Resources
- UK
CropNet - The UK Crop Plant Bioinformatics Network
- Bioinformatics at the Roslin Institute
Databases
Human-genome
databases
- Draft
Human Genome @ UCSC
- Ensembl
- Human
Transcript Database
- GDB
- GeneCards
Gene-expression
databases
- Bodymap (human and mouse genes)
- SAGE @ NCBI
- Stanford Microarray Database
- HuGE, Human GEne Expression Index
- Architecture
GeneX
Mostly plant genome
- Maize
Targeted Mutagenesis Database
- Leach/DR
gene collection
- The
Sanger Centre : ACEDB
International
nucleotide-sequence databases
- NCBI
- EBI
- DDBJ, DNA Data Bank of Japan
Other
sequence databases
- SWISS-PROT & TrEMBL
- PIR, Protein Information Resource
Databases
for other organisms
- TIGR Comprehensive Microbial Resource
- TIGR Microbial Database
- Saccharomyces Genome Database
- The C. elegans Genome Project
- FlyBase
- Mouse Genome Informatics
- The Arabidopsis Information Resource
- ZFIN, Zebrafish Information Network
Miscellaneous
databases
- GOLD, Genomes OnLine Database
- Cancer Genome Anatomy Project
- HUGO's Human Gene Nomenclature
- Gene Ontology Consortium
- ACUTS, Ancient Conserved UnTranslated Sequences
- ENZYME nomenclature database
- BRENDA, comprehensive enzyme information system
- The
SNP Consortium
- MethDB, DNA Methylation Database
- REBASE Restriction Enzyme Database
- The Tree of Life
Stuff below
this point is not bioinformatics-specific...
Software
development
Visualization
- Nonlinear
Magnification Home Page
Cmd-line
-> GUI
- Pise: A Web interface to Unix programs for
scientific applications
General programming
- Doxygen
(documentation generator)
- PO - Algorithms, Data Structures
- Dictionary of Algorithms, Data Structures, and
Problems
- C++ Standard Template Library Programmer's Guide
- Socket: Client/Server programming
Makefiles
- Makefile Tutorial at Ohio
State
- Indiana Univ - Bloomington,
c304 Makefiles
- Opus Software's Make tutorial
- Makefile tutorial at Rutgers
- Makefile tutorial at University of Hawaii
Fortran
stuff
- Interfacing
with C with Absoft Fortran compilers
- Visual C/C++ Calling Visual Fortran DLL Example
- Mac F2C
Sorting
- Sorting
and Searching Strings
- The Sorting Algorithm
Demo
Perl
- Comprehensive
Perl archive network (CPAN)
Open
source
- SourceForge:
Project Documentation
- GCC Home Page
- GNU:
Free Software Foundation
WWW programming
CGI
scripting
- eXtropia | Instant Web Scripts With CGI (Table
of Contents)
- Raggett's HTML guide
Mac
programming
- Sample code archive
- Code Fragment Manager (IM: PS)
- Metrowerks
Technical Support
XML
- XQL
FAQ (XML Query Language - Frequently Asked Questions)
- RE: SQL queries expressed in XML
- Baldwin tutorials: XML, Java, etc.
- Bioinformatic
Sequence Markup Language (BSML)
- rpbourret.com
- XML programming, writing, and training
- XML
Links
- XML-DBMS
- xml.apache.org
- Extensible Markup
Language (XML)
- XML
Parser for Java : another alphaWorks technology
- Expat
- XML Parser
- The Castor Project
Java
programming
- Putting a Java Interface on your C, C++, or
Fortran Code
- Java
Grande Forum
- Java Optimization
- BioJava.org - Main
Page
- java.sun.com
- The Source for Java(TM) Technology
- CONTENTS
-- Tricks of the Java Programming Gurus
- Chapter
28 -- Moving C and C++ Code to Java
- Soot: a Java Optimization
Framework
- Code
Conventions for the Java(TM) Programming Language: Contents
- Java Analysis
Studio
Numerical libraries
- Blitz++ Home Page
- LAPACK Users' Guide
-- Third Edition
- Netlib
- Linear Algebra for
Statistics Java Package
- Java Numerics: Main
- TNT
Home Page
- HyperArchive Keyword Search
Database development
Object
- OOFILE Online Home
- http://www.ozone-db.org/
Object-relational mapping
- AmbySoft Inc. Mapping Objects to Relational
Databases White Paper
RDB
- Oracle OCP Class
SRS
& Lion Bioscience
- SRS6
- SRS Documentation
- LION Bioscience - Homepage
- LION bioscience - PressReleases: TheScientificWorld
Licenses SRS from LION bioscience AG for use in Web Portal for
Scientists
- PostgreSQL
- MySQL
| Information
Statistics
resources
- Interactive
Statistical Calculation Pages
- Rice
Virtual Lab in Statistics
- StatCodes -- Visualization tools
Linux
- Debian
GNU/Linux -- The Universal Operating System
- Back to PLPTH 890 home page