BSCI 410 - Molecular Genetics

Bioinformatics and Library Resources

Instructor: Boots Quimby

Introduction

This webpage is designed to help students in BSCI 410 to find primary, scholarly literature as well as information about their gene of interest. If you have any questions about these resources please contact the Biology Librarian, Tom Harrod: my e-mail is tharrod@umd.edu or call (301) 405-7253

Using Bioinformatics Resources

There are a wide array of bioinformatics resources to help you find information about your gene of interest, many of these are produced and maintained by the National Center for Biotechnology Information (NCBI). Here are a few examples:

• BLAST - BLAST (Basic Local Alignment Search Tool) allows users to search existing nucleic acid/protein databases to find related sequences. This tool can help you to identify an unknown sequence or to find other sequences in various organisms that are homologous to an already identified sequence.
• Entrez Gene - This tool will help you to locate the chromosomal location of your particular gene of interest. Additionally, Entrez Gene records contain summaries of known characteristics for the gene product, lists of proteins which have been shown to interact with the gene of interest, and much more.
• Entrez Nucleotide - This is a database of gene sequences, type in the name of the gene that you are interested in and Entrez Nucleotide will retrieve sequences in a variety of organisms.
• Online Mendelian Inheritance in Man (OMIM) - OMIM is a one-stop shop for valuable information on human diseases and the genes associated with them. Entries in this database cover phenotypic and clinical features of the disease, genes linked to susceptibility, animal models, and much more - OMIM records also contain extensive literature references.
• ORF Finder - ORF (Open Reading Frame) Finder allows users to paste in a DNA sequence and see the corresponding amino acid sequences for each of the six possible reading frames - this will help you to identify the correct reading frame for the coding sequence of your gene.

Finding Scholarly, Primary Articles

When searching for scientific literature, it is important to discriminate between SCHOLARLY and POPULAR literature. The following information is adapted from the library's "Identifying Periodical Types" guide - click there for more information.

Here is a link which highlights some of the defining features of a Primary, Scholarly article

SCHOLARLY literature:

• contains the results of experiments performed in research labs
• is written by/for those with some knowledge in a particular field of study - a certain level of familiarity with the subject is assumed
• gives the professional affiliation of the researcher in order to establish his/her credentials in their field
• is extensively referenced - authors must cite the work of others as it pertains to their own work
• is reviewed by peers who work in the same field (i.e. "peer-reviewed")

• may be written by experts in a given field or by professional writers
• is written for a lay audience
• does not usually contain references

Additionally, it is important to understand the difference between PRIMARY and SECONDARY sources.

PRIMARY literature:

• contains an "experimental methods" section
• recounts experiments that have been been performed by the authors of the articles themselves
• contains "raw data" compiled by the authors which will usually be presented in tables or charts
• attempts to address a specific hypothesis
• has references which give pertinent background information for the hypothesis being addressed in the paper

• often takes the form of a review article
• contains a summary of experiments performed by the author as well as other researchers
• may contain tables and figures, but usually not as many as a primary source
• is a good place to go to learn about a field of study with which one is unfamiliar
• has references which give a history of the research that has been done in a specific area of study

Databases and Article Indexes

• BIOSIS Previews - BIOSIS Previews is a top source for finding articles in all of the biological sciences
• Genetics Abstracts - This database provides access to articles that cover the various aspects of genetics
• PubMed - Produced by the National Library of Medicine, PubMed extensively covers the biomedical literature
• Web of Science - This uniques database not only covers a wide scope of scientific literature, but it also allows you to find related articles by tracking the literature that cites and is cited by an article of interest.

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Plagiarism

Trying to pass off someone else's work as your own is a serious offense here at the University of Maryland - to avoid this please check out our Academic Integrity and Plagiarism web guide - penalties can be severe.

One tool that we have to help you avoid plagiarism is EndNote Web, EndNote Web is reference management tool which is available to all UMCP graduate students - to access this, simply go to the databases Web of Science and click on "My EndNote Web" to register.which will help you to manage your citations - with EndNote Webyou can download citations directly from the databases in which you find your articles and automatically create bibliographies.