Instructions and links for important tools and resources in bioinformatics. Step by step tutorials for each application are provided. Other applications are can be found on the web for each of these applications. However, we have found these to be the best tools for each particular task.
Information
Retrieval, Sequence
Analysis, Sequence Translation
Information
Retrieval, Protein Analysis,
Structure Analysis
Searching PubMed – Use PubMed to search journals and other literature on
any biological or chemical item of interest.
Full articles are not
provided in this database, only citations and abstracts are available to view.
Searching OMIM -- Use NCBI to get textural information and references to human genes and genetic disorders. It also has links to MEDLINE and other NCBI resources.
There are numerous databases around the world containing information useful for computational biologists. The main ones are: the National Center for Biotechnology Information (NCBI), the European Bioinformatics Institute (EBI), and the DNA Database of Japan (DDBJ). The following applications are tools which search these sites to find a particular sequence or to identify a sequence already known to you.
With these applications we can align two sequences, align
multiple sequences, and perform phylogenic analyses. One reason we would do
this is to determine what parts of the sequences are conserved from one species
to the next. Another reason would be to see how much an organism has diverged
from other organisms simply by comparing their DNA sequences. The more similar
two gene sequences are to one another, the more closely the organisms are
related. And the more dissimilar the two sequences, the farther the two genes
are in relation. With this application we can compare sequences to determine
how organisms have diverged possibly as a result of evolution.
Computational biologists need to
analyze their nucleotide sequences, and the best way to do that is to study the
protein product. The following programs
will either convert your DNA sequence into an amino acid (protein) sequence or
it will take your protein and convert it into its complimentary DNA (cDNA)
sequences. These protein and DNA
sequences can then be analyzed using other applications on this page.
The numerous information retrieval sites
on the Internet can give very valuable information concerning the sequence and
properties of a protein. Numerous
databases exist and each database is accessible through convenient search
programs. This section will introduce
useful sites that provide database search capabilities.
After obtaining the identity or
sequence of a protein, there are several valuable tools that allow further
analysis of the protein. Information
can be obtained concerning the characteristic properties of the proteins from
the sequence. Another valuable tool is
sequence alignment applications that establish the degree of similarity between
two proteins or multiple proteins.
Several programs have been
created that give scientists the ability to look at the three dimensional shape
of proteins and nucleotides. Examining
a protein in 3D allows for greater understanding of protein functions, as well
as providing students with a visual understanding that cannot always be conveyed
through still photographs or descriptions.
We have found that the best to date 3D program is RasMol, originally
developed by Roger Sayle. To use this
program it must first be downloaded onto your computer.
This site is funded by the National Science Foundation .