DNA AND PROTEIN DATABASES
GENERAL DATABASE INFO
- 01. Database Statistics (DDBJ)
- 02. GENBANK (NCBI)
- 03. EMBL (EBI)
- 04. DDBJ (DNA Data Bank of Japan)
- 05. SWISS-PROT (ExPasy)
- 06. UniProt (Universal Protein Resource)
- 07. Extinct organisms in GenBank
- 08. GENBANK latest release notes
- 09. NCBI Newslettter
- 10. The NCBI Handbook. Table of Contents
SEQUENCE SUBMISSION
A. Submission tools
- 01. GENBANK BankIt
- 02. GENBANK Sequin
- 03. EMBL Webin
- 04. DDBJ Sakura
B. Vector screening
- 01. VecScreen (NCBI)
- 02. Vector Scanning (EBI)
SEQUENCE RETRIEVAL
A. DNA
- 01. ENTREZ-Nucleotide query (NCBI)
- 02. SRS at EMBL-EBI, Hinxton (UK)
- 03. DNA Search (GenomeNet, Japan)
B. PROTEIN
- 01. ENTREZ-Protein query (NCBI)
- 02. SRS at EMBL-EBI, Hinxton (UK)
- 03. SWISS-PROT and TrEMBL (Switzerland)
- 04. Protein Search (GenomeNet, Japan)
- 05. RCSB Protein Data Bank (US)
ALERT SERVERS
- 01. PubCrawler
- 02. MedLibraryAlert
- 03. SWISS-SHOP alert server
GENOMICS
MICROBIAL GENOME PROJECTS
- NCBI Completed Microbial Genomes
- NCBI Microbial Genome Projects in progress
- DNA Structural Analysis of Sequenced Microbial Genomes
- GOLD Genomes OnLine Database
- TIGR Microbial Database
- DDBJ Genome Information Broker
- PEDANT complete genomes
- DDBJ Genome Information Broker
- PEDANT complete genomes
- TIGR Microbial Database
COMPARATIVE GENOMICS
- 01. COG Clusters of Orthologous Groups
- 02. TaxPlot (NCBI)
- 03. KEGG Kyoto Encyclopedia of Genes and Genomes
- COG_ Clusters of Orthologous Groups of proteins( NCBI)
- ERGO (Integrated Genomics, Inc.)
- HOBACGEN Homologous Bacterial Genes Database
- KEGG Kyoto Encyclopedia of Genes and Genomes
- LION bioscience _ Products and Services _ genomeSCOUTT
- PUMA Genome annotation
GENERAL GENOMICS
- 01. Entrez-Genome (NCBI)
- 02. Genome Monitoring Table (daily update EBI)
- BMERC Completed Genomes collected resources
- Genome Channel (Oak Ridge, US) _
- GOLD_ Genomes OnLine Database Homepage
- NCGR National Center for Genome Resources
- NIH News Release 06_26_2000
- Organism-specific Databases
- PEDANT front page
- The Human Genome, by All of the Top Cartoonists
DNA SEQUENCE ANALYSIS
A. DNA INFORMATION
- 01. IUPAC Nucleotide base codes
- 02. IUPAC nucleotide base codes
B. SEQUENCE FORMAT CONVERSION
- 01. READSEQ Sequence conversion (TIGEM, Italy)
- 02. READSEQ Sequence Conversion (BCM, US)
- 03. READSEQ Sequence Conversion (BioSino)
- 04. BCF Sequence conversion (Arizona)
C. SEQUENCE CLEANUP
- 01. JustBIO SeqCLEANER
- 02. Sequence Massager
- 03. BCF Sequence Cleaning Program (Arizona)
- 04. DNA Duster
E. INVERSE, COMPLEMENT, INVERSE COMPLEMENT
- 01. inverse, inverse complement (BCM)
- 02. inverse, complement, inverse complement (Colorado State University)
- 03. inverse, complement, inverse complement (at Molbiol.ru)
F. SEQ SHUFFLING or RANDOM SEQ GENERATOR
- 01. Random sequence generator and scrambler (molbiol.ru)
- 02. BCF Sequence shuffling Tool (Arizona)
- 03. SMS DNA shuffler
G. SEQUENCE OUTPUT
- 01. SeqCheck (sequence output, GC-content)
- 02. SMS Group DNA
- 03. Colored Sequences for Presentations
H. OTHER
- 01. Reading aloud of nucleotide sequences
- 02. Secret Coder Tool
- 03. The Sequence Manipulation Suite
ORF ANALYSIS
- 01. ORF Finder (NCBI) (US)
- 02. ORF Finder + translation (Molecular Toolkit, US)
- 03. GESTALT workbench (Weizmann, Israel)
- 04. PLOTORF (Emboss)
- 05. fgenesV (SoftBerry)
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06. TRANSLATION
- 01. TRANSLATOR at Molbiol (Russia)
- 02. TRANSLATION at EnCyclon (Korea)
- 03. TRANSLATION JustBIO (US)
- 04. TRANSLATION ExPASy (Switzerland)
- 05. TRANSLATION Molecular Toolkit (Colorado, US)
- 06. TRANSLATION (London)
- 07. TRANSLATION (Infobiogen, France)
- 08. TRANSLATION REMAP (Bioweb, Pasteur, France)
- 09. Six Frames Translation (UCDavis)
RESTRICTION ENZYMES
A. RE ANALYSIS
- 01. NEBcutter V1.0
- 02. Webcutter 2.0 (USA)
- 03. Restriction Maps (Colorado) (US)
- 04. JustBIO-SeqCUTTER
- 05. REMAP
- PlasMapper
- WatCut An on-line tool for restriction analysis, silent mutation scanning, SNP-RFLP analysis
B. REBASE
- New England Biolabs Enzyme Finder
REPEATS
- 01. Reputer
- 02. TRF Tandem Repeats Finder (Boston University)
- 03. REPFIND
- 04. SSR Simple Sequence Repeats Extractor
- 05. RepeatMasker
- Form for Oligonucleotids repeats finder
- INVERTED repeats (EMBOSS, Oxford, UK)
- PALINDROME (EMBOSS, Oxford, UK)
- TANDEM repeats (EMBOSS, Oxford, UK)
OLIGO_PRIMER ANALYSIS
- 01. OligoAnalyzer 3.0 (IDT BioTools)
- 02. PrimerQuest (IDT BioTools)
- 03. Primer3 at MIT (US)
- 04. Oligo Calculation GENSET
- 05. CODEHOP (based on multiple protein alignment)
- 09. BioTools (Integrated DNA Technologies)
- http--www.zbiomed.com-index.html
- NCBI Blast short sequence
- NetPrimer (US)
- netprlaunch
- Oligo Calculator (EMBL) - very simple
- Oligonucleotide Calculator (USA) - simple
- Osprey PCR Product Oligo Design Calculation Form
- PCR Amplification Assistant (Promega)
- PCR Box Titration Calculator v 0.93
- PCR Theory (Univ Bielefeld)
- pDRAW32 - freeware DNA cloning, sequence analysis and plasmid_DNA plotting software
- Primer Design
- Primer Selection (Image) (ALCES)
- Primer Selection (Image)
- Primer Selection (Text) (ALCES)
- Primer3 (older version)
- PrimerX Primer Design Based on DNA Sequence
- Tavi's PCR protocols
- Tm Determination (ALCES) - simple
- UCSC In-Silico PCR
- Visual Cloning 2000 (Redasoft)
- Web Primer_ DNA and Purpose Entry
- WWW GeneFisher (Germany) ___
PROMOTER PREDICTION
- Genomatix Software GmbH - GEMS Launcher
CODON USAGE
- Codon Usage Database
- Graphical Codon Usage Analyser
SKEW DIAGRAMS
- 01. GC Skew Tool
- 02. Skew plots (MIPS Munich)
GENE PREDICTION
- 01. Genie at Berkeley (US)
- 02. WebGeneMark
- 03. GENSCAN at MIT (US)
GENE EXPRESSION
- GEO Gene Expression Omnibus
- Huge Index Database
- SAGEmap
GENE REGULATION
- 01. POSSUM detects cis-elements
- 02. TFSEARCH Transcription Factor Binding Sites
- 03. Cluster Buster
- 04. Cis-elements Nucleotide Count Matrices
- 05. MotifViz
- 06. Zlab Gene Regulation Tools
- 07. McPromoter promoter prediction
- 08. CISTER Cis-element Cluster Finder
- 09. Regulatory Sequence Analysis Tools (RSAT)
PROTEIN SEQUENCE ANALYSIS
A. AMINO ACID AND PROTEIN INFORMATION
- 01. single letter amino acid codes
- 02. amino acid structures
- 03. Amino acid codes, genetic code table
- 03. genetic code table
- 04. Modified and unusual amino acids
- 05. PROWL - Amino Acid Properties
- 06. Physical-chemical AA classification (Venn diagram)
- 07. Amino acid properties (Venn diagram)
- http--www.russell.embl.de-aas-
B. MOTIFS and PATTERNS SEARCHING
- 01. SMART - Simple Modular Architecture Research Tool
- 02. Motif Scan (ISREC)
- 03. Radar Repeats in proteins
- 04. REPv1.1 Repeats in proteins
- 05. 2ZIP Leucine zipper prediction
- 06. InterProScan
- 06. TMHMM Server, v. 2.0
- 07. InterProScan
- 08. TRUST Server
- BLOCKS at Fred Hutchinson (US)
- FPAT Regular Expression Searching Protein Databases
- InterProScan
- MIPS ATLAS
- MOTIF Searching Protein and Nucleic Acid Sequence Motifs
- MOTIFS in SwissProt at IBCP (France)(WWW to EMAIL)
- NPS@ _ PATTINPROT search
- PatScan (also imperfect matches) at Argonne (US)
- PRATT at EBI (input alignment) ___
- PROSITE at EBI (Hinxton, UK))
- PROSITE at ExPASy (Switzerland)
- Protein Motifs at ALCES (US)
C. TRANSMEMBRANE DOMAINS
- 01. TMHMM Server, v. 2.0
- 02. TMpred Server (EMBnet)
- 03. TOPO2 Transmembrane Protein Display
D. HYDROPHOBICITY PLOT
- 01. Hydropathicity Plots at Colorado (US)
- Antigenicity Plot
- drawhca Hydrophobic Cluster Analysis plot
E. PROTEIN SORTING _ LOCALIZATION
- 01. PROTCOMP (SoftBerry)
- 02. PSORT (Japan)
- 03. TargetP Server v1.01
- 04. ESLpred (India)
- 05. SubLoc (China)
F. RANDOM PROTEIN GENERATOR
- ExPASy - RandSeq tool
G. MASS SPECTROMETRY
- PROWL
H. REVERSE TRANSLATION
- Entelechon - Backtranslation (according to codon usage table)
- Reverse Translation (all possibilities) (Colorado, US)
POST-TRANSLATIONAL MODIFICATION
A. PROTEIN GLYCOSYLATION
- 01. NetOGlyc 3.1 Server
- 02. NetNGlyc 1.0 Server
- 03. Glyprot
- 04. glycosciences.de
B. METHYLATION
- 01. MemoProtein Methylation Prediction
SEQUENCE ALIGNMENT
A. PAIRWISE SEQUENCE ALIGNMENT
- ALICAO - Contact-based Sequence Alignment
- ALIGN (global) at Genestream (France)
- Alignment (MichiganTech, US)
- ALION at Stanford University (USA)
- ALION protein alignment (Stanford University)
- BCM Search Launcher Pairwise Sequence Alignment
- BCM_ Pairwise Sequence Alignment
- Blast 2 Sequences (NCBI)
- Blast 2 Sequences
- LAGAN Vista Pairwise alignment
- LALIGN (local) at Genestream (france)
- LALIGN (local) at MBDC (Oxford, UK)
- LALIGN (local) at University of Virginia (USA)
- MBS - ALIGNER _ CLUSTALW interface for multiple sequence alignement (did not work on netscape n
- SBDS_ Pairwise Sequence Alignment (works only well for proteins)
- The USC Sequence Alignment Server
B. DOT MATRIX PLOT
Dot Plot THEORY
- Dot plot theory (RPI, US)
- 01. DOT PLOT (Colorado State University) (limit 20.391bp x 20.391 bp)
- 02. DOT PLOT FLAG (Taiwan)
- 03. Blast 2 Sequences
MULTIPLE ALIGNMENT SITES
- 01. CLUSTALW at BCM (USA)
- CLUSTALW at BioSino (China)
- CLUSTALW at CMBI (France)
- CLUSTALW at EBI (UK)
- DIALIGN (BiBiServ - Bielefeld University Bioinformatics Server)
- MGA Multiple Genome Aligner
- MUSCLE protein multiple sequence alignment server
- PipeAlign DbClustal
- PRALINE Multiple Sequence Alignment
- SAM_ Sequence Alignment and Modeling System
- T-COFFEE server
ALIGNMENT VISUALISATION_EDITING_FORMATTING
- 01. BoxShade Server (Switzerland)
- CINEMA (Colour INteractive Editor for Multiple Alignments) (UK)
- ESPript 2.2
SEQUENCE LOGOS
- 01. GENIO Logo
- 02. WebLogo
ALIGNMENT VISUALISATION_EDITING_FORMATTING
- BoxShade Server (Switzerland) ___
- CINEMA (Colour INteractive Editor for Multiple Alignments) (UK)
- ForCon homepage (Belgium)
- CLUSTALW at BCM (USA)
- CLUSTALW at BioSino (China)
- CLUSTALW at CMBI (France)
- CLUSTALW at DDBJ (Japan)
- CLUSTALW at EBI (UK)
- DIALIGN (BiBiServ - Bielefeld University Bioinformatics Server)
- IBC_ Multiple sequence alignment (MSA)
- MBS - ALIGNER _ CLUSTALW interface for multiple sequence alignement (did not work on netscape n
- MGA Multiple Genome Aligner
- MULTALIN + CLUSTAL at IBCP (WWW to EMAIL)
- MULTALIN at IBCP (WWW to EMAIL)
- PipeAlign DbClustal
- SAM_ Sequence Alignment and Modeling System
PREALIGNED DOMAINS
- 01. PANDIT
- 02. PFAM
SUBSTITUTION MATRICES
- 01. PAM120 matrix
- 02. PAM250 matrix
- 03. All available matrices
- 04. THEORY Substitution Matrices
cDNA to GENOMIC DNA ALIGNMENT
- SIM4 - a program to align cDNA and genomic DNA
- YASS DNA local alignment program
SEQUENCE HOMOLOGY SEARCHES
A. BLAST
- 01. BLAST at NCBI (USA)
- 02. BLAST at EBI (Hinxton, UK)
- 03. BLAST at GenomeNet (Japan)
- 04. BLAST at CMBI (NL)
- 05. BLAST2SRS retrieval tool - protein only (EMBL)
- 06. Do-It-Yourself WU-Blast
- BLAST at PIR-International Protein Sequence Database
- OWL BLAST Server
- The Statistics of Sequence Similarity Scores
B. FASTA
- 01. FASTA at EBI (Hinxton, UK)
C. OTHER
- 01. MPsrch Smith Waterman at EBI (UK)
- 02. PROPSEARCH at InfoBioSud
- 03. Cluster FLAG (cFLAG) (Taiwan)
- 04. RepeatMasker
D. BASED ON AA COMPOSITION
- AA composition_ protein search (ExPASY)
E. BASED ON 3D COORDINATES
- EMBL Dali_ email server for 3-D protein structure database searches
- ParAlign
3D PROTEIN IMAGES
PDB_RSCB Protein Data Bank
- 3DB Browser (EBI, mirror)
- 3DB Browser (France, mirror)
- 3DB Browser (Germany, mirror)
- 3DB Browser (Poland, mirror)
- 01. Entrez Structure at NCBI
- CATH (classification of protein structures)
- DALI server (EBI)
- EMBL Dali_ email server for 3-D protein structure database searches
- Entrez Structure at NCBI
- ExPASy - SWISS-3DIMAGE
- Image Library of Biological Macromolecules
- Molecules-R-US
- Pro3D download page
- PROTEIN EXPLORER (3D PDB online viewer)
- SCOP_ Structural Classification of Proteins
- Swiss-PdbViewer (download page)
- WebLab Viewer download page
SECONDARY_TERTIARY STRUCTURE PREDICTION
A. PROTEIN
- 01. Southampton - SBDS - GOR
- 02. The PSIPRED protein structure prediction server
- 03. JPRED (University of Dundee)
- 03. PredictProtein
- 04. PredictProtein
- 05. PSA Structure Prediction
- 3D-PSSM Protein Fold Recognition (Threading) Server
- CE Home Page - Combinatorial Extension
- CGG Protein sequence analysis
- CPHmodels - Homology modelling
- EMBL Dali_ email server for 3-D protein structure database searches
- GENO3D _ AUTOMATIC MODELING OF PROTEINS THREE-DIMENSIONAL STRUCTURE
- HMM-based Protein Structure Prediction, SAM-T02
- MDL Information Systems, Inc _ Chime Plug-in
- PREDATOR request form
- Protein Explorer FrontDoor
- SSCP_ based on AA composition (EMBL)
B. RNA
- 01. RNA folding (Rensselaer)
- 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)
- RNA movies (BiBiServ - Bielefeld University Bioinformatics Server)
C. TRANSMEMBRANE DOMAIN DRAWING
- 01. TMHMM Server, v. 2.0
- 02. TMpred Server (EMBnet)
- 03. TOPO2 Transmembrane Protein Display
- COMBOSA3D
- glycosciences.de - PDB2MultiGif
- Glyprot
- multiple sequence alignment Interactive Editor STRAP
- Protein Peeling
- Scooby-domain prediction
PHYLOGENY
- http--hsc.virginia.edu-achs-documents-ACHS-311.pdf
- HYPHY Package Page
- Phylogeny Programs (Joe Felsenstein's page)
- Phylogeny software (Glasgow University)
- rose random model of sequence evolution
- SplitsTree (Bielefeld, Germany)
- WebPhylip
TAXONOMY
A.RIBOSOMAL RNA
- Ribosomal Database Project II
- The rRNA WWW Server
- BIOSIS Resources Organism Names Search Form
- Introduction to Phylogeny
- NCBI Taxonomy project
- NEWT
- The Tree of Life Home Page
PROGRAMS TO DOWNLOAD
A. CLUSTALX
- ClustalX (Strasbourg, France)
- ClustalX (Weizmann, Israel)
- ClustalX homepage
B GENEDOC
- GeneDoc HomePage
C. MEGA2
- Molecular Evolutionary Genetics Analysis MEGA
D. ARTEMIS
- Artemis Release 5 (The Sanger Institute, UK)
- Download Java 2 SDK, Standard Edition, v 1.4.2 (J2SE)
E. SIMPLOT
- SimPlot page
F. BIOEDIT
- BioEdit Sequence Alignment Editor for Windows 95_98_NT
G. CHIME 3D
- Chemscape Chime_ download page
- HIV-1 protease -- structure with indinavir
- Molecular Tutorials using Chemscape Chime from MDL Information Systems
H. GENEDOC
- GeneDoc HomePage
I.JAVA
- Download Java 2 SDK, Standard Edition, v 1.4.2 (J2SE)
- Java Web Start
J. MEGA 2
- Molecular Evolutionary Genetics Analysis MEGA
K. pDRAW32
- pDRAW32 - freeware DNA cloning, sequence analysis and plasmid_DNA plotting software
L. RASMOL
- Getting RasMol_UMass Amherst
- RasMol V2.7.1.1 README
- RasMol V2.7.2 Manual
M. SEAVIEW
- SeaView
N. SeqASSEM
- IUBio Archive - SeqAssem DNA Contig Assembly Software
O. TREECON
- TREECON download page
