Fred R. Opperdoes's Bookmarks

GENE MACHINE

Compiled by Mark Van Ranst, Rega Institute, KU Leuven, Belgium

INTERNET SEARCH TOOLS Internet Search The Open Text Index Alta Vista: Main Page DejaNews Research Service - homepage excite Netsearch Lycos, Inc. Home Page NlightN Home Page! WebCrawler Searching Yahoo
DNA SEQUENCE ANALYSIS TRANSCRIPTION FACTOR BINDING SITES TFSEARCH MatInspector REPEATS Dot Plot (to itself) (ALCES) Direct repeats (BNL) Dyad repeats (stem-loop) (BNL) CODON USAGE Codon Usage Tabulated from Genbank (CUTG) Codon usage (ALCES) TRANSLATION ExPASy - Translate tool The Protein Machine Translation six frames (BNL) Six ORF maps (BNL) DNA Sequence Translation (ALCES) Nucleic Acid to Amino Acid Translation PATTERN SCAN PatScan RESTRICTION ENZYME RE ANALYSIS CUTTER (USA) CUTTER (Sweden) RE analysis at BNL RE LISTS RE search at BNL RE by site REBASE at GDB REBASE at NEB OLIGO/PRIMER ANALYSIS Oligonucleotide Vital Statistics Primer Selection (Text) (ALCES) Primer Selection (Image) (ALCES) Tm Determination (ALCES) BNL oligo/primer analysis GeneFisher Primer v2.2 (MIT) Primer v2.2 (Norway) BCM: Sequence Utilities BCM Gene Finder BCM: Gene Feature Searches PredictGenes (Darwin) GenLang linguistic sequence analyzer SBDS sequence analysis BNL DNA sequence analysis GC content (ps output) Bipartite Nuclear Localisation Sequence Locator
PROTEIN SEQUENCE ANALYSIS STATISTICAL ANALYIS ISREC SAPS server DISTANTLY RELATED REPEATS REPRO (EMBL) (WWW to EMAIL) 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 DIGESTION PRODUCTS SEARCH MassSearch: Searching SwissProt or EMBL by protein mass after digestion Protein identification 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) MOTIFS / PATTERNS SEARCHING PatScan (also imperfect matches) ISREC PatternFind (WWW to EMAIL) Motif Explorer FPAT Regular Expression Searching Protein Databases BNL motif searching MOTIFS in SwissProt at IBCP (France)(WWW to EMAIL) PRINTS BLOCKS PRODOM PROSITE at ExPASy SBASE MOTIF at GenomeNet (Japan) Protein Motifs (ALCES) SBDS sequence analysis The ProDom protein domain database BNL protein sequence analysis
SEQUENCE HOMOLOGY SEARCHES BLAST BLAST at NCBI (USA) - basic BLAST at NCBI (USA) - advanced BLAST at BCM: DNA searches BLAST at BCM: Protein searches BLAST at EPFL (Switzerland) BLAST at GenomeNet (Japan) BLAST at BioPD (Italy) BLAST at CRIHAN (France) (WWW to EMAIL) BLAST search in PRODOM BLAST-FTHOM (Hungary) (proteins only) (WWW to EMAIL) BLAST at GenQuest (US) FASTA FASTA at EBI (UK) (WWW to email) FASTA at GenQuest (US) FASTA subset search (Indiana) FASTA at BioPD (Italy) FASTA at CRIHAN (France) (WWW to EMAIL) FASTA at IBCP (France) (SwissProt only) BLITZ BLITZ at EBI (WWW to EMAIL) BIOSCAN BioSCAN: Match a named DNA sequence BioSCAN: Match a DNA Sequence BioSCAN: Match a named protein sequence BioSCAN: Match a protein sequence BASED ON AA COMPOSITION AA composition -> protein search (EXPASY) AA composition -> protein search (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
SEQUENCE ALIGNMENT MSA SBDS: Pairwise Sequence Alignment Pairwise LALIGN at EERIE (France) BCM: Pairwise Sequence Alignment BCM: Multiple Sequence Alignments BNL sequence comparison/alignment FSSP structure-structure alignment MULTALIN at IBCP (WWW to EMAIL) CLUSTALW at IBCP (WWW to EMAIL) CLUSTALW (Japan) MULTALIN + CLUSTAL at IBCP (WWW to EMAIL)
SECONDARY STRUCTURE PREDICTION RNA RNA folding (Zuker) PROTEIN Southampton - SBDS - GOR IBCP secondary structure (France) PredictProtein BCM: Secondary Structure Prediction BCM PSSP Sec structure prediction (single seq) at BML (UK) Sec structure prediction (multiple alignment) at BML (UK) SSCP: protein -> AA composition -> SS (EMBL) (WWW to EMAIL) SSCP: AA composition -> SS (EMBL) (WWW to EMAIL) TMAP (EMBL) (WWW to EMAIL)
GENERAL BIOINFORMATICS SITES BIOCIENCE vital links The Institute for Genome Research GenQuest - The Q server Welcome to GÉNÉTHON Web server Internet for the Molecular Biologist Molecular Biology Jump Station Microbiology Jump Station GENOME WORKSTATION BIOCCELERATOR Home Page Freiburg search tools MIPS: Martinsried Institute for Protein Sequences European Molecular Biology Laboratory (EMBL) GenomeNet WWW server NIH Home Page ABIM Online analysis tools BCM Search Launcher The BioSCAN Project Biologists's Control Panel Harvard Biological Laboratories Cambridge School of Biological Sciences DOE Biology Information Center The WWW Virtual Library: Biomolecules BNL Genome analysis Brookhaven National laboratory Welcome to ExPASy Biologists Search Palette Bio-wURLd Virtual Genome Center EERIE GENOME server Useful Web Sites for Molecular Biologists European Bioinformatics Institute (EBI)
TAXONOMY RIBOSOMAL RNA RDP Home Page The rRNA WWW Server NCBI Taxonomy project Bacterial Nomenclature Up-To-Date Introduction to Phylogeny The Tree of Life Home Page
DNA/PROTEIN DATABASES GENERAL DATABASE INFO DATABASE HOME PAGES DDBJ (JAPAN) GSDB (NCGR) EMBL (EBI) GENBANK (NCBI) SWISSPROT DATABASE ACTIVITIES/GROWTH Database growth curves Comparison of database activities The 100Kb Club SEQUENCE RETRIEVAL DNA GENBANK using ENTREZ GENBANK at NCBI GENBANK at BNL EBI-SRS Sequence Retrieval System DDBJ DNA Database of Japan BIOSCAN DBGET Integrated Database Retrieval System GSDB: Accession number query GSDB: More complicated queries PROTEIN ENTREZ Protein query SWISS-PROT OWL-Web PIR-Web - The Protein Identification Resource SWISSPROT at BNL EBI-SRS Sequence Retrieval System BIOSCAN DBGET Integrated Database Retrieval System SEQUENCE SUBMISSION GSDB: WebSub GENBANK BankIt EBI (EMBL) DDBJ Sakura 3D PROTEIN IMAGES SCOP: Structural Classification of Proteins FSSP NRL_3D-Web Molecules-R-US PDB At A Glance The NIH Molecular Modeling Home Page ExPASy - SWISS-3DIMAGE Protein Science KINEMAGE database Image Library of Biological Macromolecules EMBL Dali: email server for 3-D protein structure database searches PEDRO'S BIOMOLECULAR RESEARCH TOOLS Pedro (original site in US) Pedro (mirror in Germany) Pedro (mirror in Switzerland) Pedro (mirror in Japan) Pedro (mirror in US)


Last updated: 10 August 1997.

created by :Fred Opperdoes

GENE MACHINE

Compiled by Mark Van Ranst, Rega Institute, KU Leuven, Belgium

INTERNET SEARCH TOOLS

DNA SEQUENCE ANALYSIS

TRANSCRIPTION FACTOR BINDING SITES

REPEATS

CODON USAGE

TRANSLATION

PATTERN SCAN

RESTRICTION ENZYME

RE ANALYSIS

RE LISTS

OLIGO/PRIMER ANALYSIS

PROTEIN SEQUENCE ANALYSIS

STATISTICAL ANALYIS

DISTANTLY RELATED REPEATS

DARWIN

DIGESTION PRODUCTS SEARCH

PROTEIN SORTING / LOCALIZATION

ISO-ELECTRIC POINT / MOLECULAR WEIGHT

AMINO ACID COMPOSITION

MOTIFS / PATTERNS SEARCHING

SEQUENCE HOMOLOGY SEARCHES

BLAST

FASTA

BLITZ

BIOSCAN

BASED ON AA COMPOSITION

DARWIN

SEQUENCE ALIGNMENT

SECONDARY STRUCTURE PREDICTION

RNA

PROTEIN

GENERAL BIOINFORMATICS SITES

TAXONOMY

RIBOSOMAL RNA

DNA/PROTEIN DATABASES

GENERAL DATABASE INFO

DATABASE HOME PAGES

DATABASE ACTIVITIES/GROWTH

SEQUENCE RETRIEVAL

DNA

PROTEIN

SEQUENCE SUBMISSION

3D PROTEIN IMAGES

PEDRO'S BIOMOLECULAR RESEARCH TOOLS