| Name | URL | Category | Description | Availability | Platforms | Contact person | Institution | Remarks | Reference | |
| A list of bioinformatic courses | http://linkage.rockefeller.edu/wli/bioinfocourse/ | Course | A list of bioinformatic courses | links | ||||||
| Biocomputing Course Resource List : Course Syllabi | http://www.techfak.uni-bielefeld.de/bcd/Curric/syllabi.html | Course | A collection of links towards biocomputing course syllabi | links | ||||||
| BioComputing Hypertext Coursebook | http://www.techfak.uni-bielefeld.de/bcd/Curric/ | Course | The following set of tutorial texts has been developed for the award-winning VSNS-BCD BioComputing Courses, aimed at a mixed audience of biologists, computer scientists, and students + researchers of related areas, on a late undergraduate / graduate level. | web page; postscript | ||||||
| Blocks | http://blocks.fhcrc.org/ | Database | Motif database | web page | ||||||
| Entrez | http://www.ncbi.nlm.nih.gov/Entrez/ | Database | Entrez is a retrieval system for searching several linked databases. | |||||||
| Expasy | http://www.expasy.ch/ | Database | The ExPASy (Expert Protein Analysis System) proteomics server of the Swiss Institute of Bioinformatics (SIB) is dedicated to the analysis of protein sequences and structures as well as 2-D PAGE | |||||||
| PDB | http://www.rcsb.org/pdb/ | Database | The worldwide repository for the processing and distribution of 3-D biological macromolecular structure data. | database | ||||||
| Pfam | http://www.cgr.ki.se/Pfam/ | Database | Protein families database of alignments and HMMs | |||||||
| PROSITE | http://www.expasy.ch/prosite/ | Database | Motif database | web page | ||||||
| RegulonDB | http://www.cifn.unam.mx/Computational_Biology/regulondb/ | Database | Transcriptional regulation in Escherichia coli and predictions in all other bacteria | web page | Julio Collado-Vides | collado@cifn.unam.mx | Universidad Nacional Autonoma de Mexico | |||
| SRS | http://srs.ebi.ac.uk | Database | Multiple database querying and analytic tools | |||||||
| The University of Minnesota Biocatalysis/Biodegradation Database | http://umbbd.ahc.umn.edu/ | Database | Microbial biocatalytic reactions and biodegradation pathways primarily for xenobiotic, chemical compounds | web page | Lynda Ellis | BBDMaster@mail.ahc.umn.edu | ||||
| GeneMark | http://opal.biology.gatech.edu/GeneMark/ | Gene finding | A family of gene prediction programs. | web page | Mark Borodovsky's | Georgia Institute of Technology | prokaryotes and eukaryotes; programs are trained in an organism-specific way | |||
| GlimmerM | http://www.tigr.org/software/glimmerm/ | Gene finding | GlimmerM is a gene finder developed specifically for small eukaryotes with a gene density of around 20%. Currently, the system is trained for Plasmodium falciparum (the malaria parasite), Arabidopsis thaliana, Oryza sativa (rice), and Aspergillus. | web page | ||||||
| Grail | http://compbio.ornl.gov/Grail-1.3/ | Gene finding | Oak Ridge National Laboratory | |||||||
| GrailEXP | http://grail.lsd.ornl.gov/grailexp/ | Gene finding | Oak Ridge National Laboratory | |||||||
| Cluster | http://rana.lbl.gov/downloads/Cluster.zip | Microarray | Perform a variety of types of cluster analysis and other types of processing on large microarray datasets. Currently includes hierarchical clustering, self-organizing maps (SOMs), k-means clustering, principal component analysis. | download | windows | Michael Eisen | mbeisen@lbl.gov | University of California at Berkeley (UCB) | Eisen, M. B., Spellman, P. T., Brown, P. O. & Botstein, D. (1998). Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A 95(25), 14863-8. | |
| DNA-arrays analysis tools | http://bioinfo.cnio.es/dnarray/analysis/ | Microarray | sample correlation plot, hierarchical, self-organising neural network, various tree viewers | web tools | ||||||
| Eisen lab | http://rana.lbl.gov/ | Microarray | web page | Michael Eisen | mbeisen@lbl.gov | University of California at Berkeley (UCB) | ||||
| ScanAlyze | http://rana.lbl.gov/downloads/ScanAlyze.zip | Microarray | Process fluorescent images of microarrays. Includes semi-automatic definition of grids and complex pixel and spot analyses. Outputs to tab-delimited text files for transfer to any database. Written by Michael Eisen. | download | windows | Michael Eisen | mbeisen@lbl.gov | University of California at Berkeley (UCB) | ||
| Software comparison | http://ihome.cuhk.edu.hk/~b400559/arraysoft.html | Microarray | Comparison of microarray analysis and database softwares comparison | web page | yfleung@cuhk.edu.hk | |||||
| Software comparison | http://www.ncgr.org/genex/other_tools.html | Microarray | web page | |||||||
| Stanford microarray database | http://genome-www5.stanford.edu/MicroArray/SMD/ | Microarray | SMD stores raw and normalized data from microarray experiments,
as well as their corresponding image files. In addition, SMD provides interfaces for data retrieval, analysis and visualization. Data is released to the public at the researcher's discretion or upon publication. |
database | ||||||
| TreeView | http://rana.lbl.gov/downloads/TreeView.zip | Microarray | Graphically browse results of clustering and other analyses from Cluster. Supports tree-based and image based browsing of hierarchical trees. Multiple output formats for generation of images for publications. | download | windows | Michael Eisen | mbeisen@lbl.gov | University of California at Berkeley (UCB) | Eisen, M. B., Spellman, P. T., Brown, P. O. & Botstein, D. (1998). Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A 95(25), 14863-8. | |
| Expression Profiler | http://ep.ebi.ac.uk/ | Microarray analysis | web tools | Jaak Vilo | vilo@ebi.ac.uk | European Bioinformatics Institute | ||||
| ArrayExpress | http://www.ebi.ac.uk/microarray/ArrayExpress/arrayexpress.html | Microarray database | ArrayExpress is a public repository for microarray based gene expression data. | database | Alvis Brazma | brazma@ebi.ac.uk | European Bioinformatics Institute | Under construction | ||
| GeneX | http://genex.ncgr.org/ | Microarray database | An open source gene expression database. | download | ||||||
| The Brown lab | http://cmgm.stanford.edu/pbrown/ | Microarray resources | web page | |||||||
| GMEP | http://rana.lbl.gov/downloads/gmep | Microarray; sequence analysis |
Compute genome-mean expression profiles from expression and sequence data. | download | unix | Michael Eisen | mbeisen@lbl.gov | University of California at Berkeley (UCB) | Chiang, D. Y., Brown, P. O. & Eisen, M. B. (2001). Visualizing associations between genome sequences and gene expression data using genome-mean expression profiles. Bioinformatics 17(Suppl 1), S49-55. | |
| SDSC Biology Workbench | http://workbench.sdsc.edu/ | Package | The WorkBench allows biologists to search many popular protein and nucleic acid sequence databases. Database searching is integrated with access to a wide variety of analysis and modeling tools, all within a point and click interface that eliminates file format compatibility problems. | web page | bwbhelp@sdsc.edu | San Diego Supercomputer Center | ||||
| Phylip | http://evolution.genetics.washington.edu/phylip.html | Phylogeny | PHYLIP is a free package of programs for inferring phylogenies. It is distributed as source code, documentation files, and a number of different types of executables. | download | Unix, Windows | Joe Felsenstein | joe@genetics.washington.edu | University of Washington | ||
| Phylip on the web | http://sdmc.krdl.org.sg:8080/~lxzhang/phylip/ | Phylogeny | web page | |||||||
| Phylip on the web | http://bioweb.pasteur.fr/seqanal/phylogeny/phylip-uk.html | Phylogeny | web page | |||||||
| TreeView | http://taxonomy.zoology.gla.ac.uk/rod/treeview.html | Phylogeny | Tree drawing software for Apple Macintosh and Windows, and Linux | download | windows; Mac; linux | Roderic D.M. Page | r.page@bio.gla.ac.uk | University of Glasgow | ||
| BLAST server | http://www.ncbi.nlm.nih.gov/blast/ | Seaarch sequences in databases | BLAST server. The different versions and flavours of BLAST are implemented. | web page | blast-help@ncbi.nlm.nih.gov | NCBI | Altschul,
S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. (1990). Basic
local alignment search tool. J Mol Biol 215(3), 403-10. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25(17), 3389-402. |
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| TMHMM | http://www.cbs.dtu.dk/services/TMHMM/ | Secondary structure | Prediction of transmembrane helices in proteins | web page | ||||||
| clustal | ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalX/ | Sequence alignment | download | |||||||
| dotter | http://www.cgr.ki.se/cgr/groups/sonnhammer/Dotter.html | Sequence alignment | Dotter is a graphical dotplot program for detailed comparison of two sequences. | download | Unix, Windows | Erik L.L. Sonnhammer and Richard Durbin | ||||
| SignalP | http://www.cbs.dtu.dk/services/SignalP/ | Sequence analysis | Predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive prokaryotes, Gram-negative prokaryotes, and eukaryotes. The method incorporates a prediction of cleavage sites and a signal peptide/non-signal peptide prediction based on a combination of several artificial neural networks. | web page | ||||||
| RSA-Tools | http://rsat.ulb.ac.be/rsat/ | Sequence analysis; transcriptional regulation |
A series of tools for the analysis of reegulatory sequences. | web page | Jacques van Helden | van-helden.j@univmed.fr | Universite Libre de Bruxelle | van Helden, J., Andre, B. & Collado-Vides, J. (2000). A web site for the computational analysis of yeast regulatory sequences. Yeast 16(2), 177-87. | ||
| GDE | http://ftp.bio.indiana.edu/soft/molbio/unix/GDE/ | Sequence editing | download | |||||||
| EMBOSS | http://www.hgmp.mrc.ac.uk/Software/EMBOSS/ | Software suite | The European Molecular Biology Open Software Suite. EMBOSS is a package of high-quality FREE Open Source software for sequence analysis | download | Unix | |||||
| R | http://www.r-project.org/ | Statistics | Statistical package with many librairies, including some specific librairies for the analysis of microarray data | download | Unix, Windows, Mac | |||||
| CATH | http://www.biochem.ucl.ac.uk/bsm/cath_new/ | Structure | Database of structure classification | web page | ||||||
| CE | http://cl.sdsc.edu/ce.html | Structure | Structure comparison and alignment | web page | ||||||
| chime | http://www.umass.edu/microbio/chime/ | Structure | Chime is a free program to show molecular structure in three dimensions. | plug-in | ||||||
| PredictProtein | http://cubic.bioc.columbia.edu/predictprotein/predictprotein.html | Structure | A collection of tools for predicting secondary and tertiary protein structure. | web page; download | Burkhard Rost | Columbia University Bioinformatics Center | ||||
| Protein explorer | http://molvis.sdsc.edu/protexpl/index.htm | Structure | Software for looking at macromolecular structure and its relation to function | download | ||||||
| Rasmol | http://www.bernstein-plus-sons.com/software/rasmol/ | Structure | download | Unix, Windows, Mac | ||||||
| Rasmol | http://www.umass.edu/microbio/rasmol/rasquick.htm | Structure | RasMol Quick Start | tutorial | ||||||
| SCOP | http://scop.mrc-lmb.cam.ac.uk/scop/ | Structure | Database of structure classification | web page | ||||||
| Rasmol quick start | http://www.umass.edu/microbio/rasmol/rasquick.htm | Structure tutorial | RasMol Quick Start | web page | ||||||
| Rasmol help | http://www.umass.edu/microbio/rasmol/softhelp.htm | Structure tutorials | Liks to various Rasmol tutorials | web page | ||||||