• National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov/).
• Entrez (http://www.ncbi.nlm.nih.gov/Entrez/).
• Nucleotide, Protein, MedLine.
• BLAST (http://www.ncbi.nlm.nih.gov/BLAST/).
• Psi-Blast, BlastN, TBlastN, BlastX, TBlastX, BLAST 2 sequences, Microbial genomes.
• Orf finder (http://www.ncbi.nlm.nih.gov/gorf/gorf.html).
• Human genome browser at UCSC Genome Bioinformatics. (aka. Golden Path; ENCODE)
• Ensemble (http://www.ensembl.org/) - genome browser from EMBL-EBI-Sanger Center.
• EMBL.
• Cross database fetch (http://www.ebi.ac.uk/cgi-bin/emblfetch)
• PIR (Protein Information Resource) (http://pir.georgetown.edu/).
• Search for your own pattern (motif)  in a protein database (http://pir.georgetown.edu/pirwww/search/patmatch.html).
• European Bioinformatics Institute.
• EBI alignment database.
• ClustalW (http://www.ebi.ac.uk/clustalw/) - Remote alignment at EBI, or download a unix or windows version of ClustalW.
• Dali server (http://www.ebi.ac.uk/dali/) - Searches for structural homology.
• PDB database of 3D structures (http://www.rcsb.org).
• ExPASy (EXpert Proteomics Analysis SYstem) (http://us.expasy.org//).
• at The Swiss Institute of Bioinfomatics (SIB) (http://www.isb-sib.ch/).
• The Swiss PDB viewer (http://www.expasy.ch/spdbv/mainpage.html) - a powerful protein structure viewer and editor for Windows systems.
• A tutorial for the Swiss PDB viewer (http://www.usm.maine.edu/~rhodes/SPVTut/index.html).
• Softberry (http://www.softberry.com/berry.phtml) - A large collection of genome analysis tools accessed over a browser interface.  Free use to academic institutions limited to 50 executions per day for the entire institution.  Start by reading the software summary pdf file (near upper left corner of top window).

• Bo Demeler's Bioinformatics page. (locally supported programs)
• General documentation (General connections, ssh, webmail).
• Genomics (DNA star, Vector NTI, Oligo, GCG, Emboss & mse, Phred/phrap, Hmmer, Phylip, Topo, SAM).
• Structure (Insight II, Modeler, Shake and Bake, Hydro).
• Local blast (web interface to blast on local mirror of ncbi databases - this will work during periods when ncbi bogs down.  You need your username and password corresponding to a bcf account).
• Ultrascan.
• Database engines (Oracle, MySQL).
• Obtaining accounts.

• International Committee on Virus Taxonomy.
• The Jackson Laboratory & Mouse Genome Database.
• B. subtilis genome.
• Berkeley Drosophila Genome Project.
• Flybase.
• Yeast (cell cycle).
• T4-like phages (http://phage.bioc.tulane.edu/).

• Genedoc.
• Felsenstein's page, Phylip, & Index to phylogeny programs.
• Willi Hennig Society.
• Run Phylip at Pasteur.
• Run ClustalW at EBI.
• PAUP. (6/14/02).
• Ribosomal RNA Database (http://rdp.cme.msu.edu.) at the Center for Microbial Ecology at Michigan State University (http://www.cme.msu.edu).
• PAML (Phylogenetic Analysis by Maximum Likelihood). - Can be used to judge relative quality of  alternative trees by Maximum Likelihood, or to estimate best shape factor for a gamma correction.
• Tree of Life.
• Mega.
• HyPhy phylogeny package (http://www.hyphy.org/)
• Treeview (http://taxonomy.zoology.gla.ac.uk/rod/treeview.html) -views tree files with scale and without needing sequences
• PHYML (http://atgc.lirmm.fr/phyml/) - web site doing maximum likelihood trees.

• RepBase.
• Repeat Masker.

• Sanger Sequencing Centre.
• Pfam.
• Wash U St. Louis Genome Center.
• Oklahoma's Adv. Ctr. for Genome Tech. (Bruce Roe's Center).
• MIT Center for Genome Research.
• BCM Human Genome Sequencing Center.
• U. Washington Genome Center.
• The Human Genome Project at UCSC.
• DOE Joint Genome Institute (http://www.jgi.doe.gov/sequencing/index.html).
• Community Sequencing Program (http://www.jgi.doe.gov/CSP/index.html).
• Genome data (http://genome.jgi-psf.org/index.html).
• Microbial Genomics (http://genome.jgi-psf.org/microbial/).
• IMG phylogenetic profiler (http://img.jgi.doe.gov/cgi-bin/pub/main.cgi) [use Firefox]
• Among genomes they have sequenced, this resource allows a search for genes contained in named genomes and absent in other named genomes under a definable blast threshold.

• At Marshfield Clinics.
• CEPH database.

• Human, Drosophila, Zebrafish. at Sloan-Kettering Computational Biology Center.
• RNA families database. at Sanger Institute.

• PDB database of 3D structures (http://www.rcsb.org).
• ExPASy (EXpert Proteomics Analysis SYstem) (http://expasy.cbr.nrc.ca/).
• at The Swiss Institute of Bioinfomatics (SIB) (http://www.isb-sib.ch/).
• The Swiss PDB viewer (http://www.expasy.ch/spdbv/mainpage.html) - a powerful protein structure viewer and editor for Windows systems.
• A tutorial for the Swiss PDB viewer (http://www.usm.maine.edu/~rhodes/SPVTut/index.html).
• DSSP database and programs for making a standard assignment of seconary structure and other things from 3D data (http://www.cmbi.kun.nl/gv/dssp/).

• TIGRFAMs
• HHPred
• PROSITE (http://expasy.cbr.nrc.ca/prosite/) (http://ca.expasy.org/prosite/) - curated motif-defined familes, and some profiles.
• SBASE Protein families by nonseeded cluster analysis (http://hydra.icgeb.trieste.it/sbase/).
Parent site: International Centre for Genetic Engineering and Biotechnology (ICGEBB) (http://www.icgeb.trieste.it/).
• PRODOM - PSI-blast results seeded with Pfam. (http://protein.toulouse.inra.fr/prodom.html).
• Pfam - Curated profiles, extended sets from searching with the profiles, and other domains from PRODOM.
• Pfam at Sanger Center (http://www.sanger.ac.uk/Software/Pfam/).
• Blocks - Automatically constructed motifs from the various protein family databases.
• (http://blocks.fhcrc.org/).
• Parent site is  Fred Hutchison Cancer Research Center ( http://www.fhcrc.org/ ).
• ProtoMap (http://protomap.stanford.edu/) - hierarchical clustering of all sequences in SwissProt.
• SMART (http://smart.embl-heidelberg.de/) - profiles from curated alignments of signaling domains.
• PRINTS (http://umber.sbs.man.ac.uk/dbbrowser/PRINTS/) - groups motifs together into a fingerprint which is used to search for a domain or family.
• Interpro (http://www.ebi.ac.uk/interpro/) - a database that collates information from Pfam, PRINTS, PROSITE, ProDom, SMART, and the SWISS-PROT + TrEMBL protein databases.
• Molecular Information Agent (http://mia.sdsc.edu/). It launches a mass search against about 50 databases.  An accession number for Swiss Prot or PDB is probably the best search key for it, but NCBI accession numbers, keywords, or even sequence is accepted as a search key.  Also, they have an excellent list of web sites for relevant databases.
• Protein multiple alignment:
• Clustalw.
• T-Coffee. Web server - basic protein multiple alignment.
• T-Coffee. - program download.
• Muscle.
• SAM.
• Weblogo (http://weblogo.berkeley.edu/).

Procaryotic promoter prediction. (http://www.fruitfly.org/seq_tools/promoter.html).
• tRNAscan-SE (http://lowelab.ucsc.edu/tRNAscan-SE/)
• Alternative site.
• Coils server at EMBnet (http://www.ch.embnet.org/software/COILS_form.html) for coiled coil prediction from sequence.
• SAM - Sequence Alignment and Modeling tool. (http://www.cse.ucsc.edu/research/compbio/sam.html)
• Hidden Markov Models applied to alignment and family definition.
• Parent site is the UCSC Computational Biology Group (http://www.cse.ucsc.edu/research/compbio/).
• Psipred (http://bioinf.cs.ucl.ac.uk/psipred/) - secondary structure prediction from sequence alone.
• Also transmembrane topology detection and GenTHREADER (profile based fold recognition) at this site.
• Parent site is Bionformatics unit at University College London  (http://bioinf.cs.ucl.ac.uk/).
• Prof Liao's Bioinformatics Group.  (Dr. Li Liao, Univ. of Deleware) Servers: TMMOD (transmembrane topology), CASA (Alignment accuracy), QC-COMP (comparison of HMMs).
• TMHMM. (http://www.cbs.dtu.dk/services/TMHMM-2.0/). Transmembrane helix prediction.
• Consurf (http://consurf.tau.ac.il/) - Server for the Identification of Functional Regions in Proteins by Surface-Mapping of Phylogenetic Information.
• NIH Center for Molecular Modeling (http://cmm.info.nih.gov/modeling). - Particularly note index of tutorials for modeling programs.
• Codon usage database.
• GeneMark (http://opal.biology.gatech.edu/GeneMark/).
• BioBase - (http://www.gene-regulation.com/).
• Has taken over TRANSFAC, a database of transcription factor binding sites and various programs for using the database. Free for academic use, but also there is a "professional" version for a fee.
• Regulatory Sequence Analysis tools.
• Stastical Analysis of Protein Sequence (SAP) (http://www.isrec.isb-sib.ch/software/SAPS_form.html).
• MyHits - An interface to a variety of protein domain databases that includes some capacity for a private workspace and includes both motif scanning and profile scanning.
• GRAIL - neural network for prediction of coding sequences, taking account of p(A) sites, repetitive sequences, and CpG islands.
• Parent site: Computational Biology at Oak Ridge National Laboratory (http://compbio.ornl.gov/) - at the last inspection of this site it appears to have become dated. The help manual is off line.
• Grail search page (http://compbio.ornl.gov/Grail-1.3/).
• At the parent site, see also:
• GrailEXP - Grail supplemented with EST searching.  Also attempts to predict alternative splicing.
• Genome catalogue and genome channel - genome browsers.
• Pipeline - Grail coupled to blast search annotation.
• Domain Parser - diagnoses domains in a PDB entry by residue proximity.
• PROSPECT - a threader including position-specific score matrixes, secondary structure fitting, contact potentials, and alignment gap penalties.
• EmbNet.
• Biotoolkit - An index to many online resources..
• UCSC Computational Biology - Includes access to SAM.
• Staden Seq. Assembly Programs.
• Phred/Phrap.
• PDraw (http://www.acaclone.com). - Freeware for drawing plasmids, primer design, and restriction mapping.
• Notes on use.
• Primer3 - PCR primer picking program at MIT.
• Microarray Construction guide.
• VISTA (genomic sequence and annotation alignment package) (http://www-gsd.lbl.gov/vista/)
• Bioinformatics tutorials at IMIM.  (http://genome.imim.es/main/seminars.html#SEM)
• Indexes to useful links:
• Andrew Kropinski's review of online sequence analysis tools (http://molbiol-tools.ca/).
• Search Mol. Biol. sites from ExPasy. (BioHunt).
• Amos' WWW links page (http://www.expasy.ch/alinks.html)
• Pedro's Biomolecular Research Tools.

Macromolecular Crystallography Links at NIDDK.
• Computational biology at NIH.
• Index of software-containing sites.
• EBI biocatalog of software sites.
• Index of modelling software.
• San Diego Supercomputing Center (http://www.sdsc.edu/).
• Martin Firth's Index of bioinformatics tools ( http://sullivan.bu.edu/~mfrith/tools.shtml ); home page = (http://sullivan.bu.edu/~mfrith/).
• ATCC (http://www.atcc.org/) - Repository of strains of all kinds.
• Dave Lapointe's web server: (biotools.umassmed.edu).
• BioGrid ( http://biogrid.uta.edu/ ). - A UT Arlington supercomputing initiative.
• Experimental protocols:
• Protocols on line (http://www.protocol-online.org/)
• NWFSC molecular biology protocols (http://micro.nwfsc.noaa.gov/protocols/)
• Cell and Molecular Biology online (http://www.cellbio.com/protocols.html).
• Microbiology Information (http://www.microbes.info/).
• Sites with downloadable genome annotation GUIs
• Genomorama (http://public.lanl.gov/jgans/genomorama/)
• GBROWSE (http://www.gmod.org/?q=node/71).
• Software related to displaying or simulating biological or regulatory networks.
• Systems Biology Markup Language (SBML).
• BioTapestry.
• Dizzy.
• BioCyc (comprehensive curated collection of metabolic pathways and other systems information from multple organisms).
• PathwayAssist, aka Pathway Studio.  Expensive commercial software.
• Cell Designer. Biochemical pathway tool.
• www.systems-biology.org.
• Sites related to microarray data and related expression studies:
• Significance Analysis of Microarrays (SAM)
• Description/references (http://www-stat.stanford.edu/~tibs/SAM/).
• Web page for the developer: Dr. Rob Tibshirani.
• TIGR-Mev (MultiExperiment Viewer) (http://www.tm4.org/mev.html).
• Part of TM 4 microarray software suite (http://www.tm4.org/index.html).
• at TIGR (http://www.tigr.org/).
• DAVID-EASE
• Link obtained from Dr. Harris.  This is EASE, which is a downloadable. (The home page from this link says that it's no longer supported and redirects you to the page below).
• Home page. (http://david.abcc.ncifcrf.gov/home.jsp). (This is Database for Annotation, Visualization and Integrated Discovery, online version).
• The current version is called DAVID2006.
• Douglas A Hosack, Glynn Dennis Jr., Brad T Sherman, H Clifford Lane and Richard A Lempicki. Identifying biological themes within lists of genes with EASE. Genome Biology 2003, 4(9):R60.
• The Exact Fisher Test.
• Statistics at Square One,  Ninth Edition, T. D. V. Swinscow, Revised by M J Campbell, University of Southampton.
• Gene Set Enrichment Analysis (GSEA).
• Includes software to determine if a gene set shows significancant differences between two measured states, and the MsigDB molecular signature database.
• Systems Biology Workbench. A programming system; can run under MS Windows.
• home page. aka sys-bio.org, Computational Systems Biology @ Keck Graduate Institute
• Bioconductor. A software package written in R for microarray data analysis.
• LIMMA.
• Vista and rVista.
• Vista tabulates homology of mammalian genomes.
• rVista "combines transcription factor binding sites database search with comparative sequence analysis.
• Microbial genome alignment.
• Integrated Microbial Genomes. (IMG).
• DOE Joint Genome Institute. (JGI)

• Bioinformatics (http://bioinformatics.oupjournals.org/).
• J. Mol. Biol.
• Molecular Phylogenetics and Evolution.
• Nature Genetics.
• Mammalian Genome.
• International Mammalian Genome Society (http://www.imgs.org).
• Molecular Biology and Evolution.
• Society for Molecular Biology and Evolution.
• Genetics.
• Faseb Journals.
• ASM Journals.
• PNAS.
• J. Biol. Chem..
• Virology.

• Google Webmaster Tools
• UNIX/Linux Commands:
• linuxselfhelp (http://www.linuxselfhelp.com/)
• primer.
• List of Linux commands.
• Another list of Linux commands.
• UNIX tutorial (http://www.telecompricer.com/article/Tutorial-on-Unix.html).
• linux documentation project (http://tldp.org/).
• Webreference (http://www.webreference.com/).
• San Antonio Linux Users Group (http://satlug.org)
• Try man -k <generic keyword>
• Vi editor:
• Summary of commands - SCH (http://biochem.uthscsa.edu/~hs_lab/frames/vi.).
• Vi lovers home page (http://www.thomer.com/thomer/vi/vi.html).
• Most common vi commans.
• DIG lookups (http://www.analogx.com/contents/dnsdig.htm).
• GCG implementation at UTHSCSA.
• Cygwin (unix emulator for windows system) (http://www.cygwin.com/).
• How to do html.
• Official html ref at http://www.w3.org/hypertext/WWW/MarkUp/MarkUp.html.

• PuTTY - Windows clients for SSH and SCP (http://www.chiark.greenend.org.uk/~sgtatham/putty/).
• Perl for Windows, and other Active State software (http://www.activestate.com/).
• MacPerl runs on classic Mac. MacPerl has routines to do Mac-like interfacing built in. Os X ships with a perl installed but without the Mac-like interface routines. Addition of the Mac interface to Os X perl requires installing Mac::carbon from CPAN.
• Os X Faq (http://www.osxfaq.com) Useful Os X reference.
• BioPerl (library of perl routines for genomics applications).
• Index to bioinformatics software that operates under linux. (http://bioinformatics.org/mol_linux/index.php3).
• Microsoft technical information.
• Apple technical information.
• Compaq technical information.
• Greek Characters and Symbols.
• Fortran Market.
• Borland.
• Free Software Foundation (GNU).
• WinQVT/Net.
• GIF Constructor.
• Chem Draw.
• ZoneAlarm (firewall program from Zonelabs; http://www.zonelabs.com).
• Ad-Aware (Spyware removal; freeware and for fee versions)
• Printing at the structure center. (6/14/02).
• Exporting display from SGI's for X windows (6/14/02).
• Bioclusters - a news group concerning implementing bioinformatics software (https://bioinformatics.org/pipermail/bioclusters/).
• Host is bioinformatics.org (https://bioinformatics.org/), a non-profit organization with lots of bioinformatics projects.
• EMBOSS news group (http://www.hgmp.mrc.ac.uk/Emboss/HYPERMAIL/emboss/).
• Generic model organism database construction set (genome browser software) (http://www.gmod.org/).
• Lam-mpi documentation. (http://www.lam-mpi.org/)
• Information about shutting down windows "services" (http://www.blackviper.com)
• Standard port number assignments (http://www.iana.org/).
• UltraVNC (free client to access bcf desktop).

Misc. Bookmarks:

• Mysql databases on bioinf
• NIH commons
• Ultrascan.
• Ultrascan data.
• Junkbusters.
• Dental Biochem page.
• MedLine.
• Exchange rates.
• Material Safety Data Sheets.
• NIH.
• csr Phone & e-mail directory.
• NIH directory.
• Recombinant DNA guidelines.
• referral office (when you don't get your assignment letter) is (301)435-0715.
• NHGRI Program Announcements.
• NSF.
• NSF funding related to the Recovery and Investment Act.
• Congressional directory.
• Bestfares.com.
• Express News.
• San Antonio traffic.
• San Antonio weather (http://www.weather.com/weather/local/USTX1200).
• language translation dictionaries.
• World maps.
• San Antonio Cancer Institute.
• Wild about Texas Wildflowers (http://lone-star.net/wildflowers/index.html).
• PBase (a photographer's forum for posting photos)
• Correct time (http://www.time.gov/).
• US postal rates
• Sch tech. notes.
• Local tv guide listings.
• Stock market index

• Jef D. Boeke.
• Francois Bonhomme.
• Marshall H. Edgell.
• Thomas H. Eickbush.
• Andrew P. Hinck.
• NMR ref page.
• NMR protocols.
• HNCACB pulse program, version 5/28/02.
• Clyde A. Hutchison III.
• Haig H. Kazazian, Jr..
• Sandra L. Martin.
• Sue Naylor's chromosome 3 database (http://apollo.uthscsa.edu).
• Curtis Suttle (http://www.ocgy.ubc.ca/~suttle/).
• Holly A. Wichman.

Search engines

• all4one (http://all4one.searchallinone.com/) - coordinates a search of multiple search engines.
• Yahoo.
• Webcrawler.
• AllTheWeb.
• Google.
• Lycos.
• Excite.
• Altavista.
• Hotbot.
• ixquick (www.ixquick.com) - coordinates a search of multiple search engines.
• Thelinks (index of engines).
• Math documents.
• Dogpile (multi site search).
• Thunderstone (index of web sites).
• Internet Public Library.
• Infoplease (encyclopedia, dictionary, thesaurus).
• American/British spelling differences
• GO.com.
• Mapquest.
• Infospace (search for businesses).
• Web MD.
• Healthopedia.
• Search of Mol. Biol. sites at ExPasy.

Companies

• Biotech Industry Supplier Registry (A compilation of biotech suppliers).
• 5'->3';now Eppendorf 5 prime
• AB pyrosequencing
• Ambion
• Applied Biosystems, Perkin Elmer, PE Biosystems
• Beckman
• BiosupplyNet
• Boehringer-Mannheim (Roche)
• Clonetech (BD Biosciences).
• Genemachines (Genomic Solutions)
• InVitrogen (http://www.invitrogen.com) Through a series of mergers includes Life Technologies, Gibco, Panvera, and BRL.
• Li-Cor
• New England Biolabs
• Novagen
• Pharmacia (Amersham)
• Promega
• Stratagene
• Worthington Biochemical Corp. (http://www.worthington-biochem.com/).

UTHSCSA links.

• GSBS forms (not where the red book says they are).
• Change passwords
• Who's Where List 2-13-09.
• A-Z List 2-13-09.
• UTHSCSA Top page (http://www.uthscsa.edu).
• UTHSCSA Inside (http://inside.uthscsa.edu/) - entry page for UTHSCSA personel.
• NT password must be 8-14, have number, upper case, and lower case.  Can not be used last 12 months and can not include name, username, social security number, and ?.
• Grants management (http://research.uthscsa.edu/osp/).
• ARP/ATP login page (http://www.arpatp.com/Online/).
• Cayuse profile page
• Cayuse instructions & login
• grants.gov
• NSF FastLane
• UTHSCSA core facilities .
• Instructions for using AV system in 409L.
• Committee directory (2005-2006).
• AV support (http://www.uthscsa.edu/ais/tnt/..\learning/av.html)
• Faculty senate (http://www.uthscsa.edu/facultygovt/)
• Room scheduling [includes the dental school course schedules]  (http://studentservices.uthscsa.edu/academicinfo/roomsch.html).
• Web for faculty (but no longer used for grading courses).
• International affairs instructions for dealing with visas.
• Flex accounts Flexben, and other site for forms.
• 2004 benefits newsletter: (http://www.utsystem.edu/egi/newsletter/jan2004.htm)
• UT system insurance information
• Biomedical Summer Undergraduate Research Experience (B-SURE) program.
• Retirement plan information.

Last update: 05/23/09; Last major revision 2/14/05

Stephen C. Hardies home page.