Dicas de sites para bioinformática

Bookmarks for Marc Van Ranst

Marc Van Ranst's bookmarks used in bioinformatics courses, workshops, and lectures in Leuven, Prague, and Kalmar.

DNA/PROTEIN DATABASES

GENERAL DATABASE INFO

Database Statistics (courtesy of DDBJ)
Human Genome Sequencing 
GENBANK (NCBI)
EMBL (EBI)
DDBJ (DNA Data Bank of Japan)
SWISS-PROT (ExPasy) 
Extinct organisms in GenBank
DBGET Database Document: GenBank

SEQUENCE SUBMISSION

Vector screening

VecScreen (NCBI)
Vector Scanning (EBI)
Vector Screening System (DDBJ)
GENBANK BankIt
GENBANK Sequin
EMBL Webin
DDBJ Sakura

SEQUENCE RETRIEVAL

DNA

ENTREZ-Nucleotide query (NCBI)
SRS at EMBL-EBI, Hinxton (UK)
DNA Search (GenomeNet, Japan)

PROTEIN

ENTREZ-Protein query (NCBI)
SRS at EMBL-EBI, Hinxton (UK)
Protein Search (GenomeNet, Japan)
SWISS-PROT and TrEMBL (Switzerland)
RCSB Protein Data Bank (US)
RCSB PDB Mirror Sites
PIR-Web - The Protein Identification Resource (NONACTIVE)

ALERT SERVERS

EMBL Sequence Alerting System
SWISSPROT alert server

GENOMICS

GENERAL GENOMICS

Entrez-Genome (NCBI)
Genome Monitoring Table (daily update EBI)
NCGR National Center for Genome Resources
Genome Channel (Oak Ridge, US) *
Organism-specific Databases
GOLD: Genomes OnLine Database Homepage
PEDANT front page
BMERC Completed Genomes collected resources
NIH News Release 06/26/2000
The Human Genome, by All of the Top Cartoonists

HUMAN GENOME PROJECT

NIH/NCBI HUMAN GENOME RESOURCES

The Human Genome
Entrez Genome view: MAPVIEWER
LocusLink Introduction
Human Genome Sequencing
National Human Genome Research Institute (NHGRI)
dbSNP Home Page
NCBI Contig Build and Annotation Process

ENSEMBL (EBI/Sanger Institute)

Ensembl Genome Server

HUGO (Human Genome Organisation)

HUGO homepage
HUGO human chromosomes page
HUGO Gene Nomenclature Committee (HGNC)

OMIM (Online Mendelian Inheritance in Man)

OMIM - Online Mendelian Inheritance in Man

GENECARDS

GeneCards (Weizmann Institute, Israel)
GeneCards mirror (Finland)
GeneCards mirror (Germany)
GeneCards mirror (Canada)
GeneCards mirror (Japan)

DDBJ/CIB HUMAN GENOMICS STUDIO

DDBJ/CIB Human Genomics Studio

HGSC Human Genome Sequencing Center (Baylor College of Medicine)

Welcome to Baylor HGSC

ONL Oak Ridge National Laboratory

Human Genome Landmarks Poster
Human Genome Project Information

ETHICAL, LEGAL, SOCIAL ASPECTS

Clinical and patient aspects (HUGO)
Ethical, Legal and Social Implications (ELSI; NHGRI at NIH)
Genetic Alliance, Inc.

OTHER GENOME PROJECTS

EUKARYOTIC GENOME PROJECTS

Mouse Genome Resources Page
Rat Genome Resources Page
Zebrafish Genome Resources Page
Drosophila melanogaster @ NCBI
Malaria Genetics & Genomics
C. elegans project
Arabidopsis thaliana
Trypanosoma brucei Genome Project
Leishmania Genome Network

MICROBIAL GENOME PROJECTS

PEDANT complete genomes
Entrez: microbial genomes taxonomy tree
TIGR Microbial Database
DDBJ Genome Information Broker

VIRAL GENOME PROJECTS

Complete viral genomes (NCBI)
Retroviruses

COMPARATIVE GENOMICS

PEDANT CrossGenome categories
COG: Clusters of Orthologous Groups of proteins( NCBI)
TaxPlot (NCBI)
HOBACGEN Homologous Bacterial Genes Database
WIT Home Page
KEGG Kyoto Encyclopedia of Genes and Genomes
ERGO (Integrated Genomics, Inc.)
LION bioscience | Products and Services | genomeSCOUT™

DNA SEQUENCE ANALYSIS

RESTRICTION ENZYME

RE ANALYSIS

Webcutter 2.0 (USA)
Webcutter 2.0 (Sweden)
Restriction Enzyme Analysis (SUNY) (US)
Restriction Maps (Colorado) (US)
REMAP
MBS - SeqCUTTER - On-line enzyme restriction analysis tool
MULTI-CUT Restriction Endonuclease Buffer Data Base

RE LISTS

REBASE at NEB

RE SUPPLIERS

Restriction Endonuclease Suppliers (Multi-Cut site)

TRANSLATION

DNA Sequence Translation (ALCES) (US)
MBS - Quick Protein Translator
The Protein Machine (EBI) (UK)
ExPASy - Translate tool (Switzerland)
Nucleic Acid to Amino Acid Translation (London)
Nucleic Acid to Amino Acid Translation (London - mirror)
Nucleotide to Amino Acid Conversion (IBC) (US)
Translate a DNA Sequence (Colorado) (US)
REMAP

ORF ANALYSIS

ORF Finder (NCBI) (US)
ORF and protein analysis (SUNY) (US)
Translate a DNA Sequence (Colorado) (US)

GENE PREDICTION

GENSCAN at MIT (US) ***
PredictGenes (Darwin) (Switzerland)
BCM Gene Finder (US)
WebGeneMark
GrailEXP at Oak Ridge (US)
Genie at Berkeley (US)
Gene Prediction Services
Shotgun Sequencing
BCM: Gene Feature Searches

OLIGO/PRIMER ANALYSIS

PCR Amplification Assistant (Promega)
WWW GeneFisher (Germany) ***
Primer3 at MIT (US)
Primer3 (older version)
Primer Selection (Text) (ALCES)
Primer Selection (Image) (ALCES)
IDT OligoAnalyzer 2.0 (US) ***
Oligo Calculator (EMBL) - very simple
Tm Determination (ALCES) - simple
Oligonucleotide Calculator (USA) - simple
GENSET OLIGOS - Oligo Calculation
Primer Calculator (USA) - very good !!
NetPrimer (US)
NCBI Blast short sequence
Visual Cloning 2000 (Redasoft)
pDRAW32 - freeware DNA cloning, sequence analysis and plasmid/DNA plotting software
PCR Box Titration Calculator v 0.93
Alkami Biosystems: Primer Design Online
Web Primer: DNA and Purpose Entry
CODEHOP
Primer Selection (Image)
MBS - Oligonucleotide Calculator (very basic)
netprlaunch
Tavi's PCR protocols

TRANSCRIPTION FACTOR BINDING SITES

TFSEARCH: Searching Transcription Factor Binding Sites (Japan)
MatInspector (Germany)
Alibaba2 (Germany)

REPEATS

Dot Plot Analysis THEORETICAL EXPLANATION
Dot Plots (Colorado State University) (limit: 20.391bp x 20.391 bp)
Dot Plot (to itself) (ALCES) (postscript/GIF output)
Blast 2 Sequences (NCBI)

CODON USAGE

Codon Usage Database
Codon usage (ALCES)

PATTERN SCAN

PatScan

CONTIG ASSEMBLY

CAP sequence assembly at Infobiogen
CAP Sequence Assembly at BCM Search Launcher

SIMPLE NUCLEOTIDE MANIPULATIONS

Reverse/Inverse/Inverse complement (Colorado State University)
BCM: Sequence Utilities (inverse, complement)
MBS - SeqCLEANER - Clean up your sequences from databases marks
The Sanger Centre : Java View ABI traces at Sanger

PROTEIN SEQUENCE ANALYSIS

AMINO ACID/PROTEIN INFORMATION

single letter amino acid codes
amino acid structures

HYDROPHOBICITY PLOT

Hydropathicity Plots at Colorado (US)

REVERSE TRANSLATION

Reverse Translate a Protein at Colorado (US)

MOTIFS / PATTERNS SEARCHING

PROSITE at EBI (Hinxton, UK))
SMART - Simple Modular Architecture Research Tool
NPS@ : PATTINPROT search
PRATT at EBI (input alignment) ***
FPAT Regular Expression Searching Protein Databases
MIPS ATLAS
PatScan (also imperfect matches) at Argonne (US)
MOTIFS in SwissProt at IBCP (France)(WWW to EMAIL)
BLOCKS at Fred Hutchinson (US)
PROSITE at ExPASy (Switzerland)
Protein Motifs at ALCES (US)

GENEQUIZ

GQserve - Public GeneQuiz Server ***

GeneQuiz results folder (temporary)

GeneQuiz results for HPV16E1
GeneQuiz results for HPV16L1
GeneQuiz results for ccr5

PREDICTPROTEIN

The PredictProtein server
PPstatus: What is the PP backlog ?

DARWIN

Darwin, a Computational Biochemistry Research Tool
TreeGen: Tree generation from distance data
AllAll: Related peptide sequences
AllAllDB: Querying the all-against-all database of SwissProt
NuclPepSearch: Searching SwissProt for a nucleotide sequence
PepPepSearch: Searching SwissProt for a peptide sequence
darwin: Run a Darwin program

STATISTICAL ANALYIS

Statistical Analysis of Protein Sequences at EBI (Hinxton, UK)
SAPS at ISREC (Switzerland)

DIGESTION PRODUCTS SEARCH

MOWSE
PROWL
MassSearch: Searching SwissProt or EMBL by protein mass after digestion

PROTEIN SORTING / LOCALIZATION

PSORT (Japan)

ISO-ELECTRIC POINT / MOLECULAR WEIGHT

protein -> pI and MW (EXPASY)
pI and MW -> protein search (EXPASY)

AMINO ACID COMPOSITION

Protein -> AA composition (SBDS)
Protein -> AA composition + analysis (SAPS at ISREC)
AA composition -> protein search (EXPASY)
AA composition -> protein search (EMBL)
AA composition -> Sec. Str. (EMBL) (WWW to EMAIL)
MBS - ProtCALC - protein parameters (pI, MW, aa composition, Extinction data)
ProtoMap - Main
CGG Protein sequence analysis

SEQUENCE ALIGNMENT

PAIRWISE SEQUENCE ALIGNMENT

BCM: Pairwise Sequence Alignment
LALIGN (local) at Genestream (france)
ALIGN (global) at Genestream (France)
Blast 2 Sequences (NCBI)
SBDS: Pairwise Sequence Alignment (works only well for proteins)
MBS - ALIGNER : CLUSTALW interface for multiple sequence alignement (did not work on netscape navigator)

MULTIPLE SEQUENCE ALIGNMENT

BCM: Multiple Sequence Alignments
ClustalW at EBI (UK)
GeneBee ClustalW 1.75
CMBI CLUSTAL W
IBC: Multiple sequence alignment (MSA)
SAM: Sequence Alignment and Modeling System
CLUSTALW at GenomeNet (Japan)
CLUSTALW at DDBJ (Japan)
CLUSTALW at IBCP (WWW to EMAIL)
MULTALIN at IBCP (WWW to EMAIL)
MULTALIN + CLUSTAL at IBCP (WWW to EMAIL)
MBS - ALIGNER : CLUSTALW interface for multiple sequence alignement (did not work on netscape navigator)

ALIGNMENT VISUALISATION/EDITING/FORMATTING

BoxShade Server (Switzerland) ***
CINEMA (Colour INteractive Editor for Multiple Alignments) (UK)
ForCon homepage (Belgium)

SEQUENCE HOMOLOGY SEARCHES

BLAST

NCBI BLAST Home Page (new)
BLAST nucleotide [BLASTn] at NCBI (new)
BLAST protein [BLASTp] at NCBI (new)
BLAST at NCBI (USA) - basic
BLAST at NCBI (USA) - advanced
PSI BLAST at NCBI (USA) - Position Specific Iterated BLAST
BLAST at EBI (Hinxton, UK)
BLAST at GenomeNet (Japan)
BLAST at BCM: DNA searches
BLAST at BCM: Protein searches
BLAST at PIR-International Protein Sequence Database
BLAST search in PRODOM
OWL BLAST Server
GeneBee Basic BLAST 2.0
Genebee Advanced BLAST 2.0

FASTA

FASTA at EBI (Hinxton, UK)
FASTA at NPS (France)
Fasta 3.3

SW (Smith-Waterman)

Smith-Waterman (EBI)

BASED ON AA COMPOSITION

AA composition: protein search (ExPASY)
AA composition: PropSearch (EMBL)

DARWIN

AllAll: Related peptide sequences
AllAllDB: Querying the all-against-all database of SwissProt
NuclPepSearch: Searching SwissProt for a nucleotide sequence
PepPepSearch: Searching SwissProt for a peptide sequence
PROPSEARCH (EMBL) (WWW to EMAIL)
EMBL Dali: email server for 3-D protein structure database searches

SECONDARY/TERTIARY STRUCTURE

3D PROTEIN IMAGES

PDB/RSCB Protein Data Bank

RCSB Protein Data Bank at SDSC (main)
RCSB Protein Data Bank at Rutgers (mirror)
RCSB Protein Data Bank at NIST (mirror)
RCSB Protein Data Bank (all mirror sites)
3DB Browser (EBI, mirror)
3DB Browser (UK, mirror)
3DB Browser (Germany, mirror)
3DB Browser (Poland, mirror)
3DB Browser (France, mirror)
PDB Retriever at DDBJ
Entrez Structure at NCBI
ExPASy - SWISS-3DIMAGE
PROTEIN EXPLORER (3D PDB online viewer)
Swiss-PdbViewer (download page)
Pro3D download page
SCOP: Structural Classification of Proteins
CATH (classification of protein structures)
WebLab Viewer download page
DALI server (EBI)
Molecules-R-US
Image Library of Biological Macromolecules
EMBL Dali: email server for 3-D protein structure database searches

SECONDARY/TERTIARY STRUCTURE PREDICTION

RNA

RNA folding (Zuker)
RNA folding (Zuker, older version, allows variable temp)
RNA folding (Zuker; mirror at Wayne State University)
RNA folding (Zuker; mirror in Australia)
returns results per email only.

PROTEIN

Southampton - SBDS - GOR
BCM: Secondary Structure Prediction
PredictProtein
IBCP secondary structure (France)
Protein Explorer FrontDoor
3D-PSSM Protein Fold Recognition (Threading) Server (UK)
3DPSSM Results for Porin
CPHmodels - Homology modelling
PREDATOR request form
BCM PSSP
SSCP: based on AA composition (EMBL)
TMAP (EMBL) (WWW to EMAIL)
Description of SSThread WWW service
GENO3D : AUTOMATIC MODELING OF PROTEINS THREE-DIMENSIONAL STRUCTURE
EMBL Dali: email server for 3-D protein structure database searches
CE Home Page - Combinatorial Extension
MDL Information Systems, Inc | Chime Plug-in

TAXONOMY

NCBI Taxonomy project
The Tree of Life Home Page
Introduction to Phylogeny

RIBOSOMAL RNA

Ribosomal Database Project II
The rRNA WWW Server

PHYLOGENY

Phylogeny Programs (Joe Felsenstein's page)
Phylogeny software (Glasgow University)
TreeTop - Phylogenetic Tree prediction
CMBI CLUSTAL W

PROGRAMS TO DOWNLOAD

pDRAW32

pDRAW32 - freeware DNA cloning, sequence analysis and plasmid/DNA plotting software
pDRAW32 - freeware DNA cloning, sequence analysis and plasmid/DNA plotting software
pDRAW32 - freeware DNA cloning, sequence analysis and plasmid/DNA plotting software

SEQUIN

FTP Directory: ftp://ftp.ncbi.nlm.nih.gov/sequin/

CHROMAS

CHROMAS download page (Technelysium Pty Ltd)

ISYS

ISYS Software Homepage

BIOEDIT

BioEdit Sequence Alignment Editor for Windows 95/98/NT

GENEDOC

GeneDoc HomePage

SEAVIEW

SeaView

SEQVERTER

GeneStudio: SeqVerter

FORCON

FORCON download page
The online ForCon manual

MEGA 2

Molecular Evolutionary Genetics Analysis MEGA

TREECON

TREECON download page

RASMOL

RasMol V2.7.2 Manual
Getting RasMol/UMass Amherst
RasMol V2.7.1.1 README

CHIME 3D

Chemscape Chime: download page
Molecular Tutorials using Chemscape Chime from MDL Information Systems
HIV-1 protease -- structure with indinavir

NETSCAPE

Netscape Products: How to Download Via FTP
Upgrade to Netscape 6.1

BIOINFORMATICS SITES-LISTS

Swiss-Quiz Molecular Biology Quiz
Swiss-Jokes
The CMS-SDSC Molecular Biology Resource - San Diego (US)
SDSC Biology Workbench
MBS - Molecular Biology On-line tools selection
Molecular ToolBox
ExPASy: BioHunt
Pedro's Biomolecular research tools (original site in US)
SDSC Biology Workbench
SBDS Southampton Bioinformatics Data Server
NPS@: Welcome to Network Protein Sequence @nalysis at IBCP, FRANCE
Genome Workstation (Edinburgh)
BIOCCELERATOR (Weizmann Institute)
BioWurld - Where all Bioinformatics related URLs live.
The Bioinformatics Resource - Web Site of the CCP11 project
All-in-One Seq Analyzer
AmosBairoch's WWW links page
Brookhaven National Laboratory (BNL) sites
ExPASy Molecular Biology Server
ALCES Virtual Genome Center
Useful Web Sites for Molecular Biologists
Sequence Analysis with distributed Resources (Univ. Bielefeld)
Bioinformatica: The ultimate bioinformatics hub
Colin's Research Tools
www.molbiol.net
SeWeR: Sequence Analysis using Web Resources
GeneMark (TM) - Gene prediction software programs
GeneMark - Links
University of Cambridge, Department of Pathology
moleculaire diagnostiek & pathweb
www.doubletwist.com
LabOnWeb   
Bioinformatics Software on the Web
CMBI - Home Page Main
Draft - New York Area Bioinformatics and Computational Biology Interest Group (NY-BCB)
Fun
Bioinformatik
Bioinformatics.org: Welcome
On line sequence analysis (University College London)
Nucleic Acid Information on Internet
BMERC: Computational Biology, structure prediction, functional profiles, and genome analysis.
BMERC, Links to related sites and online journals
Plant Genetics Lab, University of Gent, Belgium
Molecular Biology On-Line Resources
IUBio Archive for Biology
DNANALYZE Home Page
Bioinformatics (University of Cincinatti)

LINKS (mostly outdated) TO MY BOOKMARKS

Bioinformatics links (Fred Opperdoes, UCL)
NEE-HOW: web resources - Comprehesive Biosite Resources
Bookmarks for Fatima Cvrèková
The Sanger Centre : Java View ABI traces at Sanger
The Sanger Centre : Computational Genomics Group
Serveurs WWW : Analyse de séquences
Sequence Alignments
GeneBee Services

BIOINFORMATICS NEWS

Bioinformatics News Service
Welcome to Bioinform -- The Global Bioinformatics News Service
Welcome to GenomeWeb -- New Media for the New Biology
NCBI News
PDB Newsletter
Subscribe to Genome Technology Today!
BioWorld Online, The Worldwide Biotechnology News and Information Source
genehack: genehack
Welcome to Biotaq.com - Biotechnology information provider on Internet
snowdeal.org > {bio,medical}informatics
BIOSCI/bionet Electronic Newsgroup Network for Biology
ExPASy - Swiss-Flash Bulletins
ISCB International Society for Computational Biology
The Scientist - The News Journal for the Life Scientist
Medline Workbench - Usa Mirror
Bioinformatics (Oxford Journals Online)
hum-molgen: positions in bioscience and medicine

BIOINFORMATICS COURSES & LECTURE NOTES

Center for BioInformatics at the University of North Carolina at Chapel Hill
Biocomputing Course Resource List : Course Syllabi
Molecular ToolBox
CRC-CGF Introduction to Bioinformatics Course
HUGO education resources
Database searching (Oxford)
Database Interrogation (Oxford)
The Gene Discovery Page
S&A Bioinformatics (Uniformed Services University)
Computational Genomics:G63/.2856.002/G22.3033.006
a list of bioinformatics courses

BIOINFORMATICS INSTITUTES

MIPS Munchen Information center for Protein Sequences
TIGR The Institute for Genomic Research (Maryland)
GENETHON (France)
EMBL - European Molecular Biology Laboratory
GenomeNet (Kyoto)
Center for Biomedical Informatics (Pittsburgh)

MEDLINE/MEDICAL INFO

NCBI PubMed (US) ***
PubMed Central Home
Web of Science (article citations)
Impact factors of journals
AMEDEO: The Medical Literature Guide **
BioMedNet MEDLINE
MEDLINE Alert service (at EMBL)
The Free Medical Journals Site *
MD Consult***
LabExplorer Home Page - The Online resource for laboratory professionals
VA LIBRARY JOURNAL LIST

INTERNET SEARCH TOOLS

Google
Alta Vista
LookSmart
EL Essential Links
Northern Light Search
Research-It! - Your one-stop reference desk
Welcome to The Electric Library
Mamma: Mother of All Search Engines
The Open Text Index
Yahoo
Jeeves
Internet Search
Net Locator
DejaNews Research Service
excite Netsearch
Lycos
WebCrawler
FILEZ: great for gifs !
The Internet Sleuth
Dogpile. All results, no mess.
iSyndicate: Content Providers: All Content Providers A-Z
www.StartTips.com


DO NOT CLICK ON THIS BOOKMARK !!!!

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Netscape Search
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Ask Jeeves
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Inside Netscape

Browser Central
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Links

AOL@School
CDNOW
CNN.com
PlanetOut - Gay & Lesbian
Quicken.com
Sephora.com
Stamps.com
worldlyinvestor
How to Customize Bookmarks... 

Personal Bookmarks

 
Directory of /lehn/transp_lehninger
nature genome gateway - papers
News from Molecular Biology Support at BITS
Biology Software
Periódicos
NCBI HomePage
Igh V genes
Brazilian Genome
Kabat Database
TIGR Microbial Database
Dr. Andrew C.R. Martin's bioinformatics site
SWISS-MODEL
Converte ESD para FastA
Directory of /repository
NCBI BLAST Home Page
HIV sequence database
Embrapa - Genetic Resources and Biotechnology - Bioinformatics Home Page
Directory of /blast
fator8
bio.perl.org - Main page
Fundação Sardi - Home Page
Entrez-PubMed
fator
PRINTS
GenomeWeb - Lists of Genome Sites
ExPASy - PROSITE
The Sanger Centre Web Server
Pfam : HMM Search (St. Louis)
Wiley - Bioinformatics - Web Links
Webcast Schedule-at-a-glance
SWISS-MODEL
Fasta3
Labtam Inc. produces PC X-Server for Windows X-ThinPro, NFS, FTP, SSH software.
XXIII Reunião De Genética de Microrganismo
CNN.com - Weather
RealPlayer Home Page

Media

Real.com Radio Tuner
PHP: Downloads
PHP: PHP Tutorial
Cyclins/CDKs
Conselho Nacional de Desenvolvimento Científico e Tecnológico
HighWire
Workshop - CPqGM - FIOCRUZ
Entrez-Taxonomy