Science hot list (Andrade)

Tools for protein and nucleotide analysis

Sequence comparison

• PSI BLAST Search at NCBI
• BLAST2 server (Bork's)
• Bioccelerator at EMBL
• Query a Databank from the Université Claude Bernard - Lyon 1
• BCM Search Launcher: Protein Sequence/Pattern Searches

Sequence comparison to motifs and domains

• Prosite collects sites, patterns, and domains.
• ProDom domains database.
• Pfam is a collection of HMM from domains.
• SMART - searchable annotated module collection.
• BLOCK search.

Gene identification

• GeneMark Server
• Grail
• Gene Finder

Structure comparison

• Dali server from Liisa Holm.

Prediction of protein properties

• REPRO repeat detection, from the National Institute for Medical Research, London
• BCM Search launcher from the Baylor College of Medicine, Houston
• TMHMM transmembrane helices and topology from the CBS, Technical University of Denmark
• PredictProtein 2D/transmembrane/tmb-topology, from B. Rost.
• PSORT subcellular location from K. Nakai.

Biological Data Bases

• SRS5 @EMBL and SRS5 @EBI link many of them

  Nucleotide and protein sequences

  • Search in SwissProt
  • NCBI dbEST
  • PDB database.

  Protein structures

  • Dali domain dictionary from Liisa Holm.
  • PDBsum contains summaries and structural analyses of PDB data files.
  • CATH classification
  • FSSP database
  • SCOP: Structural Classification of Proteins

  Taxonomy

  • UCMP Web Lift to Any Taxon
  • List of species in swissprot

  Genomes

  • Lists with status (finished/ongoing/links):
    • GOLD database by Nikos C. Kyrpides.
    • by Terry Gaasterland
  • Flybase at Harvard University
  • TIGR databases.
  • Genome sizes
  • GDB is the Genome Data Base at the Johns Hopkins University School of Medicine, Baltimore, Maryland USA
  • MIPS

  Metabolic pathways

  • KEGG Encyclopedia
  • WIT (What is There) for metabolic reconstruction.

  People

  • World Directory of Crystallographers.

Bibliographic Data Bases

• CiteSeer from NEC. A large scientific literature research index including many full text papers.
• Biomednet MEDLINE search
• Entrez Browser.
• Computer Science Bibliography at the Trier University, Germany

Chemistry & Bio-

• The amino acids
• Complex Carbohydrate Research Center
• Chemistry Teaching Resources on the Internet
• A periodic table
• About glycolysis.

Genome analysis

• GeneQuiz home page and Server
• PEDANT by D. Frishman et al.
• GenProtEc E. coli database from Monica Riley et al.
• Complete Genomes analysis by Koonin et al.
• BLAST against complete genomes from Bmerc

Text analysis

• Gene Ontology Consortium
• FAQ about linguistic analysis from the Language Technology Group, Edinburgh
• Tree-Tagger from Helmut Schmid (IMS, Stuttgart University) for part-of-speech tagging.
• Text Aligner aligns two texts (that may be written in a different language)

Neurosciences

• Neurosciences on the Internet
• Cognitive Sciences, UC Irvine
• Laboratory for Computational and Biological Vision at the University of Southern California

Software manuals/tutorials/sources

Molecular Biology Software

• NJPlot for representation of philogenetic trees.
• Ariadne and Prospero from Richard Mott, for sequence to sequence comparison.
• ESPript for representation of multiple alignments and secondary structure features.
• Pedro's BioMolecular Research Tools
• HMMER - profile hidden Markov models for sequence analysis
• CINEMA Java based editor for multiple alignments
• BOXSHADE generates graphical output from multiple alignments
• LALNVIEW graphical viewer for pairwise alignments.
• MOLMOL MOLecule analysis and MOLecule display.
• The BioCatalog at EBI, a Catalogue of Molecular Biology Programs
• Belvu, X-windows viewer for multiple sequence alignments.

Other Software

• XGobi - a system for multivariate data visualization.
• Lynx - a text based web browser.
• GNU Emacs Manual
• The Stony Brook Algorithm Repository
• CGI documentation and examples.
• Using CGI scripts from perl

Geography

• The world time server gives you the time now in any place of the world.
• Earth and Moon Viewer. Watch both from any position.
• interactive world atlas and information on local time (USA only).
• MapQuest interactive map.
• Earth Viewer.
• World Map Viewer.

Languages

Computer

• The Java tutorial
• Perl, Bioperl Development List
• LaTeX and some questions about it.
  The UK TeX Archive.
• Mathematica

Human

• Notes on using gender neutral language by Carolyn Jacobson of the English Department, University of Pennsylvania
• Anagram generator
• World Wide Words, about use and abuse of the English language.
• British vs. American English.
• The Human-Languages Page
• English dictionary Hypertext Webster Interface
• English/Deutsches dictionary
• The Alternative Dictionaries
• Ethnologue Database

Document conversion

• TOM Server

Upcoming meetings and courses

• 11th International Conference on Intelligent Systems for Molecular Biology. Brisbane, Queensland, Australia (29 June -July 4, 2003)
• Functional Genomics and Disease. European Science Foundation. Prague Hilton Hotel, Czech Republic (14-17 May, 2003)

Past ones

Publishing

Journals

• BIOINFORMATICS
• Communications of the ACM
• Genome Biology
• Genome Research: Call for Papers
• The EMBO Journal
• Genes and Function
• FEBS Journals
• Journal of Artificial Intelligence Research
• Journal of Data Mining and Knowledge Discovery
• Journal of Intelligent Systems
• Journal of Molecular Biology
• Journal of Theoretical Biology
• Nature
• Neural Networks
• Nucleic Acids Research
• Protein Engineering
• Science
• A list of publishers from the University of York library.
• Free online full-text articles list from HighWire Press.

Science encyclopedias and glossaries

• BioTech's life science dictionary
• Kimball's Biology Pages
• Phylogenetics Glossary
• Encyclopedias of math and science by Eric W. Weisstein.

Science can be funny after all...

• Annals of Improbable Research and their amazing Ig Nobel Prizes
• The Caveman column in the Journal of Cell Science.