Bookmarks
01. DNA AND PROTEIN DATABASES
01. 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. Human Genome Sequencing
- 10. NCBI Newslettter
- 11. The NCBI Handbook. Table of Contents
02. SEQUENCE SUBMISSION
01. Submission tools
- 01. Bankit (GenBank)
- 02. Sequin (stand-alone software)
- 03. EMBL Webin
- 04. DDBJ Sakura
02. Vector screening
- 01. VecScreen (NCBI)
- 02. Vector Scanning (EBI)
03. SEQUENCE RETRIEVAL
01. DNA
- 01. ENTREZ-Nucleotide query (NCBI)
- 02. SRS at EMBL-EBI, Hinxton (UK)
- 03. DNA Search (GenomeNet, Japan)
02. 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)
04. ALERT SERVERS
- 01. PubCrawler
- 02. MedLibraryAlert
- 03. SWISS-SHOP alert server
02. GENOMICS
01. HUMAN GENOME PROJECT
01. NIH_NCBI HUMAN GENOME RESOURCES
- 01. Entrez Genome view_ MAPVIEWER
- 02. Human Genome Resources
- 03. Entrez Gene
- 04. dbSNP Home Page
02. ENSEMBL (EBI_Sanger Institute)
- 01. Ensembl Genome Server
03. GENECARDS
- 01. GeneCards (Weizmann Institute, Israel)
- 02. GeneCards mirror (Germany)
- 03. GeneCards mirror (Japan)
04. DDBJ_CIB HUMAN GENOMICS STUDIO
- 01. H-InvDB Annotated Human Gene Database
05. OMIM (Online Mendelian Inheritance in Man)
- 01. OMIM - Online Mendelian Inheritance in Man
06. HUGO (Human Genome Organisation)
- 01. HUGO homepage
- 02. HUGO human chromosomes page
07. HGSC Human Genome Sequencing Center (Baylor College of Medicine)
- 01. HGSC Human Genome Sequencing Center (Baylor College of Medicine)
08. ONL Oak Ridge National Laboratory
- 01. Human Genome Landmarks Poster
- 02. Human Genome Project Information
09. ETHICAL, LEGAL, SOCIAL ASPECTS
- 01. Ethical, Legal and Social Implications (ELSI; NHGRI at NIH)
- 02. Genetic Alliance
02. OTHER GENOME PROJECTS
- 01. NCBI Genomic biology
- 02. Sanger Institute Pathogen Sequencing Unit
- 03. J. Craig Venter Institute
- 04. DDBJ Genome Information Broker
- 05. PEDANT complete genomes
- 06. GOLD Genomes OnLine Database
- 07. Genome Atlas Database
- 08. BMERC Completed Genomes collected resources
03. COMPARATIVE GENOMICS
- 01. TaxPlot (NCBI)
- 02. COG_ Clusters of Orthologous Groups of proteins( NCBI)
- 03. KEGG Kyoto Encyclopedia of Genes and Genomes
- 04. PUMA2 system for genome annotation and metabolic pathway analysis
03. DNA SEQUENCE ANALYSIS
01. DNA INFORMATION
- 01. IUPAC Nucleotide base codes
- 02. IUPAC Nucleotide base codes (DDBJ)
- 03. IUPAC Nucleotide Base Codes( NCBI)
- 04. Official IUPAC rules
02. SEQUENCE FORMAT CONVERSION
- 01. READSEQ Sequence Conversion (BCM, US)
- 02. READSEQ biosequence conversion tool (EBI)
- 03. SQUIZZ sequence_alignment format converter
03. SIMPLE NUCLEOTIDE MANIPULATIONS
01. SEQUENCE CLEANUP
- 01. JustBIO SeqCLEANER
- 02. Sequence Massager
- 03. BCF Sequence Cleaning Program (Arizona)
- 04. DNA Duster
02. INVERSE, COMPLEMENT, INVERSE COMPLEMENT
- 01. inverse, complement, inverse complement (Colorado State University)
- 02. inverse, complement, inverse complement (at Molbiol.ru)
03. SEQ SHUFFLING or RANDOM SEQ GENERATOR
- 01. Random sequence generator and scrambler (molbiol.ru)
- 02. Generate A Pseudo-Random DNA String
- 03. BCF Sequence shuffling Tool (Arizona)
04. SEQUENCE OUTPUT
- 01. Colored Sequences for Presentations
05. OTHER
- 01. Reading aloud of nucleotide sequences
- 02. Secret Coder Tool
- 03. The Sequence Manipulation Suite
04. CONTIG ASSEMBLY
- CAP Sequence Assembly at BCM Search Launcher
- DNA BASER-automatic DNA contig assembly software _ Batch contig assembly, contig editing, mutation detection and sequencing, DNA sequence assembly.
- SEQUENTIX DNA Contig Assembly Software
05. ORF ANALYSIS
- 01. ORF Finder (NCBI) (US)
- 02. ORF Finder + translation (Molecular Toolkit, US)
- 03. GESTALT Workbench
- 04. fgenesV (SoftBerry)
06. TRANSLATION
- 01. TRANSLATOR at Molbiol (Russia)
- 02. TRANSLATION JustBIO (US)
- 03. BCM Six Frame Translation of Sequence
- 04. TRANSLATION ExPASy (Switzerland)
- 05. TRANSLATION Molecular Toolkit (Colorado, US)
- 06. Six Frames Translation (UCDavis)
07. RESTRICTION ENZYMES
01. RE ANALYSIS
- 01. NEBcutter V1.0
- 02. Webcutter 2.0 (USA)
- 03. Restriction Maps (Colorado) (US)
- 04. JustBIO-SeqCUTTER
- 05. PlasMapper V2.0
- 06. WatCut
- 07. Double Digest Finder, NEB
02. REBASE
- 01. REBASE Homepage
- 02. New England Biolabs Enzyme Finder
08. PATTERN AND MOTIF SCAN
- 01. PatScan
- 02. Cluster Buster
- 03. Improbizer
09. REPEATS
- 01. TRF Tandem Repeats Finder (Boston University)
- 02. Reputer
- 03. REPFIND
- 04. SSR Simple Sequence Repeats Extractor
- 05. RepeatMasker
10. OLIGO_PRIMER ANALYSIS
- 01. OligoAnalyzer v3.1
- 02. PrimerQuest
- 03. Primer3 at MIT (US)
- 04. CODEHOP (based on multiple protein alignment)
- 05. PCR Primer Design and reaction optimisation (text)
- 06. PCR Now
- 07. Primaclade
- 08. OligoCalc_ Oligonucleotide Properties Calculator
- 09. NetPrimer
11. CODON USAGE
- 01. Graphical Codon Usage Analyser
- 02. Codon Usage Database
12. SKEW DIAGRAMS
- 01. GC Skew Tool
- 02. Skew plots (MIPS Munich)
13. GENE PREDICTION
- 01. Genie at Berkeley (US)
- 02. WebGeneMark
- 03. GENSCAN at MIT (US)
14. GENE EXPRESSION
- 01. GEO Gene Expression Omnibus
15. 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)
- The Sanger Centre _ Java View ABI traces at Sanger
04. PROTEIN SEQUENCE ANALYSIS
01. AMINO ACID AND PROTEIN INFORMATION
- 01. single letter amino acid codes
- 02. amino acid structures
- 03. genetic code table
- 04. Modified and unusual amino acids
- 05. PROWL - Amino Acid Properties
- 06. Physical-chemical AA classification (Venn diagram)
- 07. Venn diagram
02. 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. TMHMM Server, v. 2.0
- 07. InterProScan
- 08. TRUST Server
03. TRANSMEMBRANE DOMAINS
- 01. TMHMM Server, v. 2.0
- 02. TMpred Server (EMBnet)
- 03. TOPO2 Transmembrane Protein Display
04. HYDROPHOBICITY PLOT
- 01. Hydropathicity Plots at Colorado (US)
- 02. DRAWHCA Draw Hydrophobic Cluster Analysis plot
05. PROTEIN SORTING _ LOCALIZATION
- 01. PROTCOMP (SoftBerry)
- 02. PSORT (Japan)
- 03. TargetP Server v1.01
- 04. ESLpred (India)
- 05. SubLoc (China)
06. RANDOM PROTEIN GENERATOR
- 01. RandSeq
07. MASS SPECTROMETRY
- 01. PROWL
08. REVERSE TRANSLATION
- 01. Entelechon backtranslation tool
- 02. Reverse Translation (all possibilities) (Colorado, US)
- 03. BENN Backtranslation Tool
09. POST-TRANSLATIONAL MODIFICATION
01. PROTEIN GLYCOSYLATION
- 01. NetOGlyc 3.1 Server
- 02. NetNGlyc 1.0 Server
- 03. Glyprot
- 04. glycosciences.de
02. METHYLATION
- 01. MemoProtein Methylation Prediction
05. SEQUENCE ALIGNMENT
01. PAIRWISE SEQUENCE ALIGNMENT
- 01. Pairwise alignment (MichiganTech, US)
- 02. BCM Search Launcher Pairwise Sequence Alignment
- 03. LAGAN Vista Pairwise alignment
- 04. ALICAO - Contact-based Sequence Alignment
02. DOT MATRIX PLOT
Dot Plot THEORY
- Dot plot theory (RPI, US)
- 01. DOT PLOT (Colorado State University) (limit 20.391bp x 20.391 bp)
03. MULTIPLE SEQUENCE ALIGNMENT
01. MULTIPLE ALIGNMENT SITES
- 01. CLUSTALW at BCM (USA)
- 02. CLUSTALW at EBI (UK)
- 03. TCoffee
- 04. MUSCLE - MUltiple Sequence Comparison by Log-Expectation
- 05. PRALINE Multiple Sequence Alignment
02. ALIGNMENT VISUALISATION_EDITING_FORMATTING
- 01. BoxShade Server (Switzerland)
- 02. CINEMA (Colour INteractive Editor for Multiple Alignments) (UK)
03. SEQUENCE LOGOS
- 01. WebLogo
04. PREALIGNED DOMAINS
- 01. Pfam
05. SUBSTITUTION MATRICES
- 01. PAM250 Mutation Matrix
- 02. THEORY Substitution Matrices
06. cDNA to GENOMIC DNA ALIGNMENT
- 01. SIM4 - a program to align cDNA and genomic DNA
06. SEQUENCE HOMOLOGY SEARCHES
01. BLAST
- 01. BLAST at NCBI (USA)
- 02. BLAST at EBI (Hinxton, UK)
- 03. BLAST at GenomeNet (Japan)
- 04. Do-It-Yourself WU-Blast
- 05. OWL BLAST Server
02. FASTA
- 01. FASTA at EBI (Hinxton, UK)
03. OTHER
- 01. MPsrch Smith Waterman at EBI (UK)
- 02. ParAlign
04. BASED ON AA COMPOSITION
- 01. AA composition_ protein search (ExPASY)
05. BASED ON 3D COORDINATES
- 01. SSM Secondary structure matching
- 02. EMBL Dali_ email server for 3-D protein structure database searches
07. SECONDARY_TERTIARY STRUCTURE
01. TERTIARY STRUCTURE DATABASES
- 01. NCBI Structure - MMDB page
- 02. DALI server (EBI)
- 03. OCA browser-database for protein structure_function
- 04. CATH database
02. SECONDARY_TERTIARY STRUCTURE PREDICTION
01. PROTEIN
- 01. COMBOSA3D
- 02. multiple sequence alignment Interactive Editor STRAP
- 03. Scooby-domain prediction
- 04. The PSIPRED protein structure prediction server
- 05. PredictProtein - Structure Prediction and Sequence Analysis
- 06. PSA Structure Prediction
- 07. Protein Explorer FrontDoor
- 08. 3D-PSSM Protein Fold Recognition (Threading) Server
- 09. CE Home Page - Combinatorial Extension
- 10. CPHmodels - Homology modelling
- 11. HMM-based Protein Structure Prediction, SAM-T06
- 12. MDL Information Systems, Inc _ Chime Plug-in
02. RNA
- 01. RNA folding MFOLD
- 02. MFOLD (Zuker; mirror in Australia)
- 03. RNA movies (BiBiServ - Bielefeld University Bioinformatics Server)
- 04. Model.it @ ICGEB Trieste
08. PHYLOGENY
- 01. PhyML_ fast, accurate estimation of large PHYlogenies by Maximum Likelihood
- 02. Phylogenetic Web repeater POWER
- 03. Phylodendron - Phylogenetic tree printer
- 04. TreeTop - Phylogenetic Tree prediction
- 05. Phylogeny Programs (Joe Felsenstein's page)
- 06. HYPHY Package Page
- 07. rose random model of sequence evolution
- 08. SplitsTree (Bielefeld, Germany)
09. TAXONOMY
RIBOSOMAL RNA
- 01. The Tree of Life Home Page
- 02. History of life through time
10. PROGRAMS TO DOWNLOAD
01. CLUSTALX
- ClustalX homepage
02. GENEDOC
- Genedoc NRBSC _ Downloads
03. BIOEDIT
- BioEdit Sequence Alignment Editor for Windows 95_98_NT
04. MEGA4
- Molecular Evolutionary Genetics Analysis MEGA
05. ARTEMIS
- Informatics Software_ Artemis
06. CHROMAS
- CHROMAS download page (Technelysium Pty Ltd)
11. MEDLINE_MEDICAL INFO
- 01. NCBI PubMed UZ Leuven link
- 02. ISI Web of Science
- 03. ISI Journal Citation Reports
- 04. XplorMed (eXploring Medline abstracts)
- 1911 encyclopedia
- AMEDEO_ The Medical Literature Guide __
- AP Photo Archive
- Best Practice of Medicine
- BiologyBrowser
- BioMedNet MEDLINE
- Corbis--stock photography and pictures
- Dermatology Image Atlas
- LabExplorer Home Page - The Online resource for laboratory professionals
- LIBIS Web-OPAC
- MD Consult___
- MGAS Fulltext
- NGC - National Guideline Clearinghouse
- PubCrawler Home Page
- PubMed Central Home
- Scientific Portraits (Dibner Library of the History of Science and Technology)
- The Free Medical Journals Site _
- UpToDateŽ
- VA LIBRARY JOURNAL LIST
- WorldPhotos - photos from all around the world
12. CHEMISTRY
- 01. PubChem Compound
- 02. ACROS template search
- 03. Super Drug Database
13. OTHER USEFUL LAB LINKS
01. DILUTION CALCULATOR
- 02. Dilution Calculator (Simple)
02. CENTRIFUGE CALCULATOR
- 01. CentrifugeHelper Version 1.1
03. RADIOACTIVITY CALCULATOR
- 01. Radioactive Decay Calculator
04. LAB PROTOCOLS ONLINE
- Protocol Online - Your lab's reference book
05. PDF MAKER
- Create PDF Online free, PDF API, PDF .NET Server, Consulting
06. SEND LARGE FILES ONLINE
- Send2deliver - File too big for e-mail_ Try Send2Deliver!
07. SCHEDULE A MEETING
- Doodle_ Schedule a meeting
- RANDOM.ORG - Generate a series of integers
VERSION 106, FEBRUARY 2008
- blaststation 10x NCBI BLAST Accelerator