Molecular Biology & Bioinformatics

Bookmark and Share

Facts and Background Information
Selected print and electronic encyclopedias, dictionaries, handbooks, etc.
Locate items in the library catalog and other libraries.
Use indexes to search for articles in journals, proceedings, etc.
Recommended academic, professional, and learned societies sites, and more.
Contact a Librarian

Below are a few major, frequently used sources for the study of Molecular Biology & Bioinformatics. Please consult with a reference librarian for directions to many more sources in your topic. The literature is international in scope and organized into primary (the first public record of the research) and secondary (works derived from primary sources) publications, although this distinction is beginning to be blurred in some web resources.

See also the research guides: Agriculture, Plant Sciences & Botany; Biology; and General Science. For additional information on sources please consult a librarian. Internet resources require a Tufts I.D. number for off-campus access (authorized users statement).


Facts and Background Information     [back to top]

Reference Resources

Abbreviations & Acronyms

A searchable database of Biotechnology abbreviations and acronyms. Includes the name of the abbreviation/acronym, the field in which it is used, and a link to a website where further information is available.

Dictionaries & Glossaries

BioTech Life Sciences Dictionary
8300+ terms dealing with biochemistry, biotechnology, botany, cell biology and genetics. Also some terms relating to ecology, limnology, pharmacology, toxicology and medicine.

Cell & Molecular Biology Online - Educational Resources: Dictionaries & Glossaries
Provides links to several online biotech and biology dictionaries.

Glossary of Biochemistry and Molecular Biology. Portland Press.
Nearly 3000 terms with succinct definitions.

2can Glossary - Bioinformatics Educational Resource
A glossary of common words found in the bioinformatics and molecular biology literature.


Encyclopedia of Life Sciences
A reference work integrating current theory and practice of all basic and applied aspects of the life sciences, with an emphasis on cell and molecular biology.

Handbooks & Protocols

Current Protocols Online
Laboratory manuals on methods giving step-by-step procedures. Tufts subscribes to the following sections only: Cell Biology, Human Genetics, Molecular Biology, Nucleic Acid Chemistry, and Protein Science.

Methods in Enzymology
A standard source for methods and protocols in molecular biology. Some topics coverd are: guide to yeast genetics and molecular biology, branch chain amino acids, recombinant DNA, molecular evolution .

Protocols-Online - Your Lab's Reference Book
Covers a broad range of biological protocols contributed by researchers world-wide, as well as Calculators & Converters, PRC related calculators, and others.


Annual Reviews in Biomedical Sciences
Eighteen annual review titles covering the major areas in the biomedical sciences. Search individual titles or across the suite of titles.

Software Review Archive - BIOSIS
Links to over 150 non-critical reviews of biological software packages.

Resources for Writing

A web-based reference/citation and bibliography manager. Allows users to keep track of and download citations from our internet databases/indexes and then use these references for writing and automatically formatting papers and bibliographies. This software works with EndNote too!

Style Manuals

Scientific Style & Format: The CBE Manual for Authors, Editors, and Publishers
[PRINT. Tisch Reference T11 .S386 1994]
The standard style guide for scientific writing. Covered are: styles, mechanics, and special scientific conventions. The section describing how to write and submit papers for journal publication has been removed to allow for the inclusion of more disciplines.

IX. The Council of Biology Editors (CBE) Style of Documentation in Science and Mathematics - The New Guide to Writing Research Papers. Monroe Community College.

Sciences: Documenting Sources

NLM Recommended Formats for Bibliographic Citations - Supplement: Internet Formats

Find Books     [back to top]

A library's catalog covers most aspects of a subject over centuries of publications in many languages. Catalogs can be searched by author, title, subject, and keyword. Tisch Library uses the Library of Congress (LC) classification scheme. LC classification brings similar books together on the shelves, which facilitates browsing. Books on Molecular Biology and Bioinformatics can be found in QH (Natural History); QK (Botany); QL (Zoology); QM (Human Anatomy); QP (Physiology); and QR (Microbiology). A fair number of them are classified in QH 506. It is important to use the catalog when looking for information pertaining to these topics.

The Catalogs

Library Catalog How To Use

Boston Library Consortium Catalogs How To Use

Harvard University Library System Catalog (HOLLIS)

National Research Council of Canada
Includes Canada Institute for Scientific & Technical Information (CISTI).

WorldCat. FirstSearch. How To Use
Click on WorldCat or select WorldCat database from the search box.
Covers almost all of the catalogs of the major research libraries, as well as public libraries.

Other Sources for Books

Books in Print
Lists books currently in print and available on the market for purchasing.

Document Delivery
Borrow from other libraries, both books and journal articles.

The Online Books Page - Call Numbers QH-QR (Biological Sciences)
A listing of books freely readable online hosted by the University of Pennsylvania Library.

Find Articles     [back to top]

To locate articles or research papers within periodicals and journals, it is necessary to use specialized databases known as indexes. Database Searching Tips (also available in PDF) provides valuable information on how to construct a search for best results.


BIOSIS Previews. ISI, 1980- How To Use
Supplies comprehensive coverage of nearly 5,500 life science journals and 1,500 items from international meetings, review articles, and books.

Cambridge Scientific Abstracts - Biological and Medical Sciences. CSA/IDS.
Select Biological and Medical Sciences and click on Quick Search to retrieve the Biological and Medical Sciences category with its seven indexes including Zoological Record Plus. Choose Biological Sciences Search Subfiles to specifically search any of its twenty-three indexes.
Please note: the National Biological Information Infrastructure has recently published a thesaurus to a number of the CSA indexes entitled NBII Biocomplexity Thesaurus.

Current Contents Connect. ISI. How To Use
An ISI current awareness database with an interdisciplinary focus; covers science, social science and humanities; includes the latest issue and table of contents from over 8,000 of the world's research journals and some evaluated scholarly websites. Can create auto alerts for e-mail updates. Has search and journal browse functions. Updated daily. Holdings are for one year.

MEDLINE. Ovid, 1966- Old Medline, 1951-1965. How To Use
National Library of Medicine's bibliographic database covering the fields of medicine, nursing, dentistry, veterinary medicine, the health care system, and pre-clinical sciences.

A service of the National Library of Medicine, the site provides access to over 12 million MEDLINE citations back to the mid-1960's and additional life science journals. PubMed includes links to many sites providing full text articles and other related resources.

Science Citation Index Expanded. ISI, 1945- How To Use
Part of the ISI Web of Science, this index provides author, subject and citation access to journal articles and book reviews in the sciences, as well as citation values for particular papers, citation tracking and related records. Updated weekly.

Scopus. Elsevier, 1966-
An index to the world's scientific, technical and medical literature (14,000 scholarly titles), including 2,700 titles in Social Science, Psychology and Economics. Updated daily. Non-English titles are covered as long as English abstracts are available. Full-text linking is available wherever the technology and the access arrangements permit and continues to expand as such arrangements allow. Integrated web searching and patent searching by Scirus.

Electronic journals

Periodicals are listed in the library catalog. Holdings in all formats are unified in one record, and most entries for journals held in electronic format contain a hyperlink to the source. Searches in the web-based catalog enable one to follow these links directly. A complete list of electronic journals is on the Tisch homepage under Electronic Journals.

Key Weekly Science Journals

Nature. Nature Publishing Group.
Current: v387-, 1997-
Back volumes v. 54-84 (1896-1910) and v.132- (1937-): [PRINT. Tisch Bound Periodicals Q1 .N2]
Back volumes v.112-131 (1923-1933): [MICROFORMS. R93]

Science. AAAS.
Current: v270-, (1995-)
Back volumes v.1-270, (1800-1995)

Collections of Electronic Journals

BioMedCentral is an independent publishing house committed to providing immediate free access to peer-reviewed biomedical research and has established 57 new titles in the biomedical sciences.

Blackwell Synergy. Blackwell Publishing.
Provides full-text access to 600+ scholarly journals. To browse Biology, select Life and Physical Sciences.

HighWire Press
Contains the full text of 335 leading biomedical journals available primarily from professional societies. Archival backfiles are open access. Subscriptions are need for the current year. Consult the library catalog to see if Tufts subscribes to the title.

ScienceDirect. Elsevier.
A database of over 1,700 journal titles covering the life, physical, technical and social sciences. Titles start with the initial volume of publication; all titles have tables of contents and abstracts, and most have full-text articles. Tufts has access to approximately 800 titles from 1995 to date. The titles formerly published by Academic Press commence with 1993. Green boxes indicate subscribed titles; white boxes are for non-subscribed titles. Please note: ScienceDirect no longer provides access to non-subscribed titles. Articles from non-subscribed titles must be obtained from Tisch Document Delivery - Borrow from Other Libraries or purchased directly from ScienceDirect. Browse the Biochemistry, Genetics, and Molecular Biology Library.

Provides access to 460+ electronic journals with full-text and some book series. The focus is on science and technology. Browse Online Libraries for titles in the Life Sciences.

Wiley InterScience
Provides full-text access to 300+ journals published by John Wiley & Sons. To browse the Life and Medical Sciences journals click on Journal Finder.

Other Sources for Research Papers

Pre-prints, conferences and proceedings, dissertations, and technical reports are other sources for original research.

ISI Proceedings How To Use
An index to the published literature of significant conferences, symposia, and seminars.

Conference Papers Index. CSA/IDS, 1982-
Citation to papers presented at major science meetings worldwide; focus is on life and environmental sciences.

Dissertation Abstracts. First Search. 1861- How To Use
Indexes dissertations accepted at accredited institutions; covers all disciplines. Updated monthly.

Tufts University Dissertations. ProQuest, 1996- How To Use
Tufts dissertations and theses published in Dissertation Abstracts from 1996 to date. Provides full-text access.

GrayLit Network. U.S. Government.
A science portal of technical reports from the Department of Energy, Department of Defense, Environmental Protection Agency, and NASA.

Patents Indexes

Derwent Innovations Index. ISI. How To Use
A resource for patent literature from 40 patent issuing authorities. Uses the ISI search interface and links forward in time to citing patents and backwards in time to cited patents. Coverage for some patents begins in 1963.

esp@cenet (Searchable Worldwide Patents Database) EPO, 1920-
Free worldwide patent information with full-text patents from the European Patent Office.

U.S. Patent and Trademark Office
Website for the USPTO. Information on patenting an idea, doing a patent search, and locating a patent depository library.

USPTO Patent Classification Home Page
U.S. Manual on Patent Classification searchable website.

Find Web Resources on the Internet

In the 1980s the World Wide Web emerged and spawned publications of its own, independent of the print traditions. Information retrieved from the open web must be reviewed for authority, accuracy and authenticity. Keeping these limitations in mind, there are some excellent information resources available from the open web, especially those associated with government agencies and universities. See how to evaluate web resources.

General Web Search Engines

Google How To Use
A top ranked web search engine, with good relevancy. Uses tabs at the top of the search box. The tab Directory is a Page Rank version of the Open Directory and includes a category for Science Biology with the subcategory Biochemistry and Molecular Biology. There is also a tab for Groups (a Usenet news database), Images and News. How To Use
Good web search engine. Indexes full webpage, PDF files, Microsoft Word files, and text within Flash files. Also includes tabs for databases of news, pictures, videos, audio and FTP files.

Science Web Search Engines

Scirus How To Use
A comprehensive science-specific search engine. Locates peer-reviewed articles.

Websites     [back to top]

Tufts University Biology Department

Communication Forums

A set of electronic communication forums for biological scientists worldwide. Hosted at the U.K. Medical Research Council's Human Genome Mapping Project Resource Center.


DBCAT, The Public Catalog of Databases
Links to existing genetics and molecular biology databases listed by main application fields: DNA, RNA, Protein, Genomic, Mapping, Protein Structure, and Literature. A collaboration of INFOBIOGEN and EBI.

Sequence Databases

BCM Search Launcher. Baylor College of Medicine.
Project to organize molecular biology-related search and analysis services available on the WWW by function by providing a single point-of-entry for related searches.

A set of similarity search programs designed to explore all of the available sequence databases regardless of whether the query is protein or DNA.

FASTA Programs at the U. of Virginia
Stands for Fast-All. Can be used for a fast protein comparison or a fast nucleotide comparison. Program achieves a high level of sensitivity for similarity searching at high speed.

Pub Crawler
A free "alerting" service that scans daily updates to the NCBI Medline (PubMed) and GenBank databases according to search terms requested by user.

Nucleotide Sequence Databases

Entrez Nucleotide. NCBI.
A collection of sequences from several sources, including GenBank, RefSeq, and PDB.

EMBL Nucleotide Sequence Database
Europe's primary nucleotide sequence resource.

GenBank. NCBI.
The NIH genetic sequence database; an annotated collection of all publicly available DNA sequences.

Genome Databases

Entrez Genome. NCBI.
Database provides views for a variety of genomes, complete chromosomes, contiged sequence maps, and integrated genetic and physical maps.

The Genome Database (GDB)
The official central repository for genomic mapping data resulting from the Human Genome Initiative. At present, GDB comprises descriptions of the following types of objects: regions, maps, and variations of the human genome.

Human Genome Browser from UCSC
Site contains the reference sequence for the human and C. elegans genomes and working drafts for the mouse, rat, C. briggsae, and SARS genomes.

KEGG: Kyoto Encyclopedia of Genes and Genomes
A suite of databases and associated software, integrating our current knowledge on molecular interaction networks in biological processes (PATHWAY database), the information about the universe of genes and proteins (GENES/SSDB/KO databases), and the information about the universe of chemical compounds and reactions.

Online Mendelian Inheritance in Man. NCBI.
A database that catalogs human genes and genetic disorders.

REBASE The Restriction Enzyme Database
A collection of information about restriction enzymes and related proteins containing published and unpublished references, recognition and cleavage sites, isoschizomers, commercial availability, methylation sensitivity, and crystal and sequence data.

Protein Sequence Databases

Entrez Protein Database. NCBI.
Compiled from a variety of sources, including SwissProt, PIR, PRF, PDB, and translations from annotated coding regions in GenBank and RefSeq.

PIR International Protein Sequence Database (PIR-PSD)
Annotated protein sequence database.

Swiss-Prot Database
A curated protein sequence database that provides annotation, minimal redundancy, and high level of integration with other databases.

Protein Structure Databases

MMDB: Molecular Modeling DataBase. NCBI.
A structure database that is a subset of three-dimensional structures obtained from the Protein Data Bank.

PIR (Protein Information Resource)
Project provides protein databases and analysis tools to support research on molecular evolution, functional genomics, and computational biology.

PIR International Protein Sequence Database (PIR-PSD)
Annotated protein sequence database.

Protein Data Bank
Repository for the processing and distribution of 3-D biological macromolecular structure data.

Protein Motif Databases

PROSITE: Database of Protein Families and Domains
Consists of biologically significant sites, patterns and profiles that help to reliably identify to which known protein family a new sequence belongs.

3-D Protein Views Databases

Molecular Visualization Software: Protein Explorer, Chime, & RasMol
Free software for visualizing the three-dimensional structures of protein, DNA, and RNA macromolecules, and their interactions and binding of ligands, inhibitors, and drugs.

Software: Molecular Graphics. Protein Data Bank.
List of molecular graphics and modeling programs.

Protemics Databases

Proteome Analysis @ EBI
Provides statistical and comparative analyses of the predicted proteomes of fully sequenced organisms.

Microarray Databases

DNA Microarray (Gene Chip)
Basics on DNA microarray technology and a list of academic and industrial links.

Protein - Other

Protein Reviews on the Web. National Center for Biotechnology Information.
Short guides on the approximately 200 human CD cell-surface molecules. Peer-reviewed; provides approximately 20 standardized categories of information (biochemical function, ligands, etc.) for each CD antigen.

Text Browsers

Entrez. NCBI.
The text-based search and retrieval system used at NCBI for the major databases, including PubMed, Nucleotide and Protein Sequences, Protein Structures, Complete Genomes, and Taxonomy.

A service of NLM, provides access to MEDLINE citations back to the mid-1960s and additional life science journals.

SRS @ EBI. European Bioinformatics Institute.
A data integration platform, providing access to the large volumes of Life Science data stored in more than 400 internal and public domain databases.

Molecular Biology Information Servers

European Bioinformatics Institute (EBI)
Center for research and services in bioinformatics. The Institute manages databases of biological data including nucleic acid, protein sequences and macromolecular structures.

European Molecular Biology Laboratory (EMBL)
Lab conducts basic research in molecular biology, supports scientists and students in its member states, and develops new instrumentation for biological research.

L. A. Hazen Genome Sequencing Center. Cold Spring Harbor Laboratory.
Center performs high-throughput sequencing of several organisms, including the flowering plant Arabidopsis thaliana, the fission yeast S. pombe, and homo sapiens.

National Center for Biotechnology Information
NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information.

Database Directories and Links

Amos' WWW links page. ExPASy Molecular Biology Server.
Pointers to information sources for life scientists with an interest in biological macromolecules.

Introduction to Molecular Biology Databases. EBI.
Describes molecular biology databases available to researchers arranged by topics such as bibliographic, nucleotide and protein sequence, structure, genetic, and taxonomy.

Molecular Biology Database Collection
From Nucleic Acids Research database issue v.31 issue 1

Gateways & Portals (Web Libraries)

All the Virology on the WWW
A collection of virology and microbiology related websites that includes online course notes (diagrams, tutorials and videos), news, and an index to virus pictures on the web. Maintained by Dr. David Sander at Tulane University Medical School.

Bioinformatics and Systems Biology Electronic Library
Papers, conferences, links to subject journals maintained by Markus Herrgard, UCSD.

The Biolist - Molecular Biology Places of Interest
Molecular biology links arranged by more than 70 categories. From BBSRC Bioscience IT Services in the UK.

Biological Servers on the Web
Index with links to biology websites including: databases, bibliographies, online tools, and tutorials.

Biology Links. Harvard University
Maintained by Harvard's Department of Molecular and Cellular Biology.

Biotechnology Information Directory. WWW Virtual Library.
Links to companies, research institutes, universities, sources of information and other directories specific to biotechnology, pharmaceutical development and related fields.

Cell and Molecular Biology Online
Provides a general resource for online information on cell and molecular biology.

Cell Biology. WWW Virtual Library.
List of websites arranged by subject.

Molecular Biology. Yahoo Directory.
Links to online resources on molecular biology. Access by subtopic, most popular, or use search function.

Government Resources

Bioethics Resources on the Web. National Institutes of Health.
A list of annotated web links pertaining to bioethics issues, such as human subject research, stem cell research genetic testing, animal care, and medicine.
A resource for information about the Human Genome project coordinated by the U.S. Department of Energy and the National Institutes of Health. Projects include the Genome to Life and Microbial Genome programs.

National Center for Biotechnology Information (NCBI). NIH.
The NCBI is a national resource for molecular biology and informatics.

National Human Genome Research Institute
Agency responsible for the support of NIH genetic and genomic research, investigating the ethical, legal and social implications surrounding genetics research, and conducting educational outreach on genomics.

National Institute of Biomedical Imaging and Bioengineering. NIH.
Coordinates with the biomedical imaging and bioengineering programs of other agencies and NIH Institutes to support imaging and engineering research with potential medical applications and facilitates the transfer of such technologies to medical applications.

National Library of Medicine
Access NLM's databases, publications, and research activities.


The Big Picture Book of Viruses
Provides links to virus pictures on the web. Search by name, structure/genome, host, or disease.

Genome Science Images. DOE.
A resource for genome illustrations, line drawings, and microscopy.

IMB Jena Image Library of Biological Macromolecules
Information on three-dimensional biopolymer structures with an emphasis on visualization and analysis. Includes access to all structures images deposited in the Protein Data Bank and Nucleic Acids Data Bank.

Klotho: Biochemical Compounds Declarative Database
Search 439 unique compounds; configurations, synonyms. Viewable as static image or in PDB format which requires a molecular viewer plug in for your browser.

Library of 3-D Molecular Structures
Molecular models of various chemical, amino acids, lipids and drugs. Some models are in PDB format for which a molecular viewer plug in is needed.

Molecular Expressions Galleria
Collections of color photographs taken through an optical microscope. From National High Magnetic Field Laboratory.


Genome News Network

Genomics: A Global Resource
News source for genomics information.

The Scientist
An international news magazine published in print and on the web that reports and analyzes the issues and events that impact the life sciences. Site contains news, features, professional information, and research updates.

Research Tools
An open-source project dedicated to providing Java tools for processing biological data

Biology Workbench. UCSD.
Web-based tool for biologists for searching popular protein and nucleic acid sequence databases. Comprised of (WWW)-based user interface, an interoperable interface to biological sequence and structure databases, a collection of biological sequence and structure analysis tools, and links to biological sequence and structure databases.
Information on free tools for bioinformatics research.

The BioToolKit. BioSupply Net.
An annotated directory of over 1000 links to online molecular biology resources; includes basic research tools and advanced applications for genome, transcriptome, and proteome data retrieval, analysis, and visualization.

CMS Molecular Biology Resource
Internet and electronic resources for molecular biology, biochemistry, biotechnology, molecular evolution, and biomolecular modeling.

Free Open Source software analysis package specially developed for the needs of the molecular biology user community. The software automatically copes with data in a variety of formats and allows transparent retrieval of sequence data from the web.

Technical Manuals. Roche Applied Science.
Commercial site with access to select manuals online as well as product listings.

WFCC-MIRCEN World Data Centre for Microorganisms
A directory of culture collections, databases on microbes and cell lines, and a gateway to biodiversity, molecular biology and genome projects.

Societies & Associations

American Crystallographic Association (ACA)
Promotes the study of the arrangement of the atoms in matter, its causes, its nature and its consequences, and of the tools and methods used in such studies.

Association of Biomolecular Resource Facilities
Promotes communication and cooperation among core facilities and research laboratories and provides research mechanisms for evaluation and improvement of biotechnical capabilities of core facilities. Site contains information on the ABRF, a yellow pages that lists commercial labs offering analytical services, and links to other websites of interest.

European Bioinformatics Institute
Center for research and services in bioinformatics that manages databases of biological information including nucleic acid, protein sequences and macromolecular structures.

Environmental Mutagen Society (EMS)
The primary scientific society fostering research on the basic mechanisms of mutagenesis as well as on the application of this knowledge in the field of genetic toxicology.

International Society for Computational Biology
Group's emphasis is on the role of computing and informatics in advancing molecular biology.

Federation of American Societies for Experimental Biology (FASEB)
Coalition of independent Member Societies that serve the interests of biomedical and life scientists, particularly those related to public policy issues.

The Human Genome Organization
Promotes international discussion and collaboration on scientific issues and topics crucial to the progress of the world-wide human genome initiative.

The Society for Mathematical Biology
A forum for discussion of research in biology, mathematical biology, and mathematics applied to or motivated by biology.

Swiss Institute of Bioinformatics
Academic non-profit foundation whose mission is to promote research, the development of databanks and computer technologies, teaching and service activities in the field of bioinformatics.

UK Human Genome Mapping Project Resource Centre
Provides access to research tools for the fields of genomics, genetics and functional genomics.

The Wellcome Trust Sanger Institute
A genome research center based in the UK. Site offers information on the institute's programs, genome databases, software tools, and other resources.

Study &Teaching Resources

BioTech. University of Texas, Austin.
Hybrid biology/chemistry educational resource and research tool.

Coalition for Education in the Life Sciences
A national coalition of professional societies in the biological sciences that have joined together to improve undergraduate education in the life sciences. Website has links to educational resources and other professional organizations.

MIT Biology Hypertextbook
Online textbook that supports MIT's introductory molecular biology course.

Molecular Biology Notebook Online
A tool for students and teachers.

DOE HGP Genomics Primers
A good basic explanation of the human genome project and its potential impact.

2can Bioinformatics Educational Resource
This site provides short and concise introductions to basic concepts in molecular and cell biology and bioinformatics. The main emphasis is placed on making it as easy as possible for the user to understand which tools and databases are available from the EBI and from sites belonging to it's collaborators.


American Type Culture Collection (ATCC)
A global nonprofit bioresource center that provides biological products, technical services, and educational programs to private industry, government, and academic organizations.

Commercial site offers both public and subscription accessed life sciences information and resources. Aggregates relevant news, information and services for industry research and development.

Commercial site with links to biomedical research supplies and services.

Dennis Kunkel's Microscopy, Inc.
Photo gallery of an award-winning photomicrographer. Extensive collection of scientific images for viewing or licensed use.

Fisher Scientific
Commercial manufacturer and distributor of scientific instruments, equipment, supplies, workstations and chemicals.

Commercial provider of technology, services and domain expertise for procurement and materials management in support of the life sciences, higher education and industrial research markets.

Contact a Librarian     [back to top]

Miriam Allman. Contact for questions about library collections.
Regina Raboin. Contact for reference questions and instruction requests.

Tufts University