Bioinformatics links

• Bioinformatics Links Directory

Source material

• PubMed
  • Hardcore PubMeding (advanced PubMed searching)
• HubMed
• PubMed Reader
• Authoratory

Bioinformatics related blogs

• Computational Biology - Bioinformatics Blogs — long list of blogs
• PostGenomic
• Notes from the Biomass
• Flags and Lollipops
• Bio::Blogs
• BioHacking
• Systems Biology & Bioinformatics
• RNA Bioinformatics
• LabAction — Human Genetics,Science Projects,Science Experiments
• Fungal Genomes and Comparative Genomics
• The Tree of Life — blog of Jonathan A. Eisen
• note2self
• BMI Students
• Flags and Lollipops
• Eye on DNA

Databases

• wikipedia:Biological_database

General

• European Bioinformatics Institute — portal for research and services in bioinformatics, with databases of nucleic acid and protein sequences, and macromolecular structures - from the EMBL, Hinxton UK.
• NCBI/GenBank (USA) — offers many important databases (PubMed, GenBank, OMIM) and some tools.
• DDBJ (Japan)
• CrossRef

Genomes

• TIGR
• JGI
• Sanger
• NCBI
• UCSC ENCODE Project (includes latest, most complete build of the Human genome)

Lists of genomes in progress

• Genome projects
• http://wit.integratedgenomics.com/GOLD/
• http://www.tigr.org/tdb/mdb/mdbinprogress.html
• Ensembl genome download (mainly Eukaryotes)
• Complete Published Genome Projects: 524

Genes / Proteins

• [http://www.ncbi.nlm.nih.gov/sites/entrez?db=OMIM Online Mendelian Inheritance in Man (OMIM)
• PPID - Protein to Protein Interaction Database
• Bioinformatic Harvester III (beta)
• iHOP - Information Hyperlinked over Proteins

Web servers

• World Index of BioMolecular Visualization Resources
• PDBSiteScan
• Catalytic Site Atlas (CSA) — a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure.
• SiteEngine — Functional Sites Structural Search Engine; Recognizes regions on the surface of one protein that resemble a specific binding site of another.
• SuMo
• ASTRAL — The ASTRAL Compendium for Sequence and Structure Analysis.
• MolMovDB — Database of Macromolecular Movements with Associated Tools for Flexibility and Geometric Analysis.
• SCOP: Structural Classification of Proteins
• Dali Fold Classification — based on exhaustive, all-against-all 3D structure comparison of protein structures in the Protein Data Bank
• PDBsum — provides an at-a-glance overview of every macromolecular structure deposited in the Protein Data Bank
• Vienna RNA Secondary Structure Prediction
• BLOCKS — a service for biological sequence analysis
• Searching for 3D functional sites in a protein structure
• wikipedia:Structural genomics

Data acquisition (search engines)

• A Periodic Table of Visualization Methods

Keyword

• SRS (tutorials can be found at http://www.icgeb.trieste.it/~netsrv/courses/RH/srs/ or http://www.no.embnet.org/Programs/DB/srs_tut.php3)
• Entrez (tutorial can be fond at http://www.ncbi.nlm.nih.gov:80/Database/tut1.html)

Similarity

• BLAST

Multiple sequence alignment

• ClustalX (ftp) (tutorial can be found at http://www.bioinf.org/molsys/ClustalX_tutorial.html)
• BioEdit
• BCM search launcher
• GCG
• Lists
• STRAP — Multiple Sequence Alignment

Prediction

• NNPREDICT — Protein Secondary Structure Prediction
• Pattern and profile searches Pattern and profile searches

Phylogenetic analysis

• PAUPp (tutorial can be found at http://paup.csit.fsu.edu/Quick_start_v1.pdf)
• Mega2
• PHYLIP
• Treeview
• List

Taxonomy

• Species 2000
• uBio — uses names and taxonomic intelligence to manage information about organisms
• BioLib — an international encyclopaedia of plants, fungi, and animals.
• Forestry Images
• The 2006 IUCN Red List of Threatened Species

Software / Scripts

• BioLinux.org
• 3DNA
• Raster3D
• EMBOSS applications
• Script List — Bioinformatics related

Other

• Bioinform — bioinformatics news service.
• Bioinformatics.ca — curated web directory of molecular biology and bioinformatics resources
• Bioinformatik — categorical web directory for bioinformatics theory - from the Univ. of Düsseldorf. Mathematics and Computer-based.
• Bioplanet Jobs — bioinformatics jobs, education resources, bulletin board, CV posting.
• Canadian Bioinformatics Resource — dedicated to providing researchers with convenient, effective access to high-quality bioinformatics tools and databases.
• CMS Molecular Biology Resources — a compendium of tools for molecular biology, biotechnology, molecular evolution, biochemistry and biomolecular modeling.
• DNA and Protein Analysis Toolkit — compendium of bioinformatics computing services from The Rockefeller University. Many different ways to analyse biomolecules.
• Genome Programs — links to online genomics resources - including the individual projects.
• Molecular Biological Sites — includes sequence search windows, as well as databases and tools related with proteomics and structural bioscience.
• Snowdeal.org — a weblog that provides daily updates and links to news items and stories of interest to bioinformatics community.
• UBC Bioinformatics Centre Resource Directory — currated and categorized database of links to the top bioinformatics and molecular biology resources on the web.
• The OpenScience Project
• Quick guide to characteristics of metal sites in proteins
• sfcheck — a program for assessing the agreement between the atomic model and X-ray data or EM map.
• OmicsWorld
• OMICS: A Journal of Integrative Biology
• ZINC — a free database of commercially-available compounds for virtual screening.
• BIO.SK - Directory

Wikis related to Bioinformatics

• Wikiomics.org — (User:Christoph)
• SNPedia
• Omics.org — an openfree wiki site for -omes and -omics in Biotechnology and Bioscience.
• OpenWetWare.org
• AAA Wiki — considers sequenced Drosophila genomes.
• openfree BioDomain.org — a list of biological domains.
• BioDirectory.com
• MyBio.net
• wikipedia:Bioinformatics
• wikibooks:Computational Biology (aka Bioinformatics)