At one time I had to travel a hundred miles to get to the nearest research library. At that time, Online searches cost significant amounts of cash! Now, at least for the medical community (and those who do research in the medical area of science), it is free to get abstracts and some of the full articles!

It has been four years since I have updated this page. It is amazing to see how much has changed on the internet. Many of the sites that I used to use are completely gone or have moved and are hard to find. It seems that many of the competing alternate sites for doing the same function are dissapearing. Today, a single centralized page predominates.

• http://www.info.sciencedirect.com/ ScienceDirect Journal search with Abstracts and some Journal articles!
• http://www.sciencedirect.com/science/journals Science journals
• http://www.info.sciencedirect.com/librarian_help/ideal_integration Science journals by field

• http://www.pubmedcentral.gov/ PubMed Central A free archive of life sciences journals
• http://www.pubmedcentral.gov/front-page/fp.fcgi?cmd=full_view A full list of journals

• http://www.nlm.nih.gov/nlmhome.html US National Library of Medicine
• http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed Pubmed Journal search, gives abstracts! Also has links to molecular biology databases of DNA/Genome/Protein sequences and 3-D structure data.

My research experience deals primarily with DNA structures and DNA information (code). The following links make my research possible!

I once loaded a program on my personal computer that took about two weeks to run. The equivalent internet tool that utilizes a supercomputer took a few seconds to a few minutes to do the same thing!

• http://www.ncbi.nlm.nih.gov/ National Center for Biotechnology Information
  • http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed Pubmed Journal search, gives abstracts! Also links to DNA/Genome/Protein sequences and 3-D structure data.
  • http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?db=Nucleotide Nucleotide database A collection of nucleotide entries from GenBank. Both from individual papers and composite sequences of more and more of the genome!
  • http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?db=Genome Genome The whole genomes of over 600 organisms. Some sequencing is in progress.
    • http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi?taxid=9606
      Homo sapiens A mapping of the human chromosomes, a genome view. The Maps are linked to nucleotide entries.
  • http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?db=Popset Popset A set of DNA sequences that have been collected to analyse the evolutionary relatedness of a population. The pop. could originate from different members of the same species, or from organisms from different species. They are submitted to GenBank via "Sequin", often as a sequence alignment.
  • http://www.ncbi.nlm.nih.gov/Tools/ Tools for data mining Tools for Bioinformatics Research.
    • http://www.ncbi.nlm.nih.gov/BLAST/ BLAST nucleotide and protein sequence similarity search tool.
    • http://www.ncbi.nlm.nih.gov/COG/ COGs Clusters of Orthologous Groups of proteins (COGs) were delineated by comparing protein sequences encoded in 21 complete genomes, representing 17 major phylogenetic lineages. Each COG consists of individual proteins or groups of paralogs from at least 3 lineages and thus corresponds to an ancient conserved domain. The presence or absence of a protein in different genomes can tell us about the "evolution" (or degradation) of the organisms.
    • http://www.ncbi.nlm.nih.gov/gorf/gorf.html Open Reading Frame Finder locates the standard and alternative stop and start codons. The deduced amino acid sequences can then be used to BLAST against GenBank.
    • http://www.ncbi.nlm.nih.gov/STS/ STS Match Program allows you to search your DNA sequence for sequence tagged site (STS), which have been used as landmarks in various types of genomic maps.
    • http://www.ncbi.nlm.nih.gov/UniGene/ UniGene UniGene is an experimental system for automatically partitioning GenBank sequences into a non-redundant set of gene-oriented clusters. Each UniGene cluster contains sequences that represent a unique gene, as well as related information such as the tissue types in which the gene has been expressed and map location.
    • http://www.ncbi.nlm.nih.gov/genemap/ Gene Map of the Human Genome An outline of the complete sequence of the human genome, the first draft of which may be available as early as 2001. GeneMap'99 includes the locations of more than 30,000 genes - about one third of all human genes. As well as assisting in assembling the complete human genome, GeneMap'99 is also of immediate use for identifying and isolating genes that contribute to human disease.
    • http://www.ncbi.nlm.nih.gov/VecScreen/VecScreen.html VecScreen is a tool for identifying segments of a nucleic acid sequence that may be of vector, linker or adapter origin prior to sequence analysis or submission. VecScreen was developed to combat the problem of vector contamination in public sequence databases.

• http://www.genome.ad.jp/ Genome Net Bioinformatics Center, Institute for Chemical Research, Kyoto University
• http://www.ch.embnet.org/index.html The Swiss node of EMBnet Swiss Institute of Bioinformatics
• http://www.ebi.ac.uk/services/index.html European Bioinformatics Institute: Services
• http://www.ebi.ac.uk/Tools/ European Bioinformatics Institute: Tool Box
• http://www.sanger.ac.uk/ The Wellcome Trust Sanger Institute: a Genome research institute using large scale sequencing and analysis

• http://clustalw.genome.jp/ Clustal W Japanese site for Multiple Sequence Alignment of DNA and protein.
• http://www.ebi.ac.uk/clustalw/ ClustalW A general purpose multiple sequence alignment program for DNA or protein.
• http://bioweb.pasteur.fr/seqanal/interfaces/clustalw.html ClustalW : Multiple Alignments
• http://www.ch.embnet.org/software/ClustalW.html ClustalW : Multiple Alignments
• http://www.ch.embnet.org/software/TCoffee.html T-COFFEE : This program is more accurate that ClustalW for sequences with less than 30% identity, but it is slower.

It is hard to keep links up to date. The following two catalogs are the most complete. When looking for interesting sites, it is best to consult both catalogs since the complement each other.

Amos' Catalog is one of the best lists of Molecular Biological sites. It is slanted toward protein structures rather than DNA information. The list is up to date however!

• http://www.expasy.ch/alinks.html Amos' Catalog (Swiss site)
• http://expasy.cbr.nrc.ca/alinks.html Amos' Catalog (Canadian mirror site)
• http://au.expasy.org/alinks.html Amos' Catalog (Australian mirror site)
• http://expasy.nhri.org.tw/alinks.html Amos' Catalog (Taiwan mirror site)

  Pedro's Catalog is also a very complete listing of Molecular Biology sites. Pedro's Catalog has many entries that are not found in Amos's Catalog! The list seems to be 9 years old at this time and the number of mirror sites has decreased. It may be on the way out.

• http://www.public.iastate.edu/~pedro/research_tools.html Pedro's Catalog (US site)
• http://www.biophys.uni-duesseldorf.de/BioNet/Pedro/research_tools.html Pedro's Catalog (German mirror site)

The following site lists various Biology sites.

• http://mcb.harvard.edu/BioLinks.html Harvard University Biology Links

If any of the links do not work please e-mail me.
WebMaster: Michael Brown
research@mhrc.net

Copyright © 1998 - 2010 by Michael Brown all rights reserved
Officially posted January 1, 1998
last revised January 1, 2010