Molecular History Research Center

Online Medical libraries

    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.

  • ScienceDirect Journal search with Abstracts and some Journal articles!
  • Bio Med Contains NIH/PubMed documents, plus a large collection of theses, dissertations, and other publications not found anywhere else for free, making it the most comprehensive free search on the web.

The Major Research Tools I Use in my Research

    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!

  • National Center for Biotechnology Information
    • Pubmed Journal search, gives abstracts! Also links to DNA/Genome/Protein sequences and 3-D structure data.
    • Nucleotide database A collection of nucleotide entries from GenBank. Both from individual papers and composite sequences of more and more of the genome!
    • Genome The whole genomes of over 600 organisms. Some sequencing is in progress.
    • 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.
    • Tools for data mining Tools for Bioinformatics Research.
      • BLAST nucleotide and protein sequence similarity search tool.
      • 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.
      • 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.
      • 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.
      • 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.
      • 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.

Service sites in Other Countries

General Purpose Sequence Alignment

Catalogs of Molecular Biology Sites on the Web.

    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!

    Also note that Amos' name is no longer being associated with the list. I would guess that the list has been updated to such an extent and the web has changed to such an extent that the present list no longer resembles Amos' original list.

    It is now called "Life Science Directory" and is being maintained by the Swiss Institute of Bioinformatics. However it is now no longer updated.

  • Life Science Directory (Swiss site)

    Pedro's Catalog was also a very complete listing of Molecular Biology sites. Pedro's Catalog has many entries that were not found in Amos's Catalog! The list is not being kept up and the number of mirror sites has decreased. It may be on the way out.

    Sure enough, the original US site now no longer exists. The only site that remains is the German mirror site which was last modified in 1995!. As of January 2011 it is still on the web. (Now in 2014 the german mirror site is also gone.

A small selection of Internet tools (links) for the Molecular Biologist. Presently the MHRC is looking at possible explanations for the formation of unprocessed pseudogenes.

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

Copyright 1998 - 2020 by Michael Brown all rights reserved
Officially posted January 1, 1998
last revised January 2, 2020