This application is useful
when the user knows the name of the protein he/she wishes to study. Many
databases contain protein sequences as well as nucleotide sequences on file
which can be searched for in the search programs of these database websites.
The easiest way to search for a protein of interest is to go to any of the
three main bioinformatics database sites (NCBI, EBI, or DDBJ) and type in a
keyword (name of protein) into the search program. Another way is to go to the
Protein Data Bank (PDB) and search for the protein there. The PDB site also
allows the user to view structures as well as sequence information.
If you know the name of a
protein, obtaining the sequence of the protein is a good way to start to gain
more information on its properties or functions. There are several sites where it is possible to obtain sequence
information, however, these direction are specific to the NCBI site. Again we
will be using the NCBI’s Entrez Search and Retrieval System.
Instructions:
1. At the top of the page, click the down arrow next to “search” and select “Proteins.”
2. In the next box type the desired protein name and click the “GO” button.
3. A list of summaries, sorted with respect to relevance, will be returned.
The summaries can
help you to determine if the description is the protein of interest.
4. Select the hyperlink to retrieve the full information.
Information is given
on the specifics of the sequence identification experiment.
5. Scroll to the bottom of the page where the sequence is located.
6. The default sequence display is “GenPept.”
There are often cases
when this form of listing cannot be copied and pasted into applications.
7. To change the
sequence format, click the down arrow next to “Display.”
There
will be several formats to choose from.
The “FASTA” format is often the most useful.
8. Highlight “FASTA” and
then mouse click the “Display” button.
When you are ready, click
here to start.
National Center for
Biotechnolgy Information (NCBI HomePage)