|
Collecting and Storing Sequences in the Laboratory – Exercise
We are going to use the Entrez search program at NCBI to perform a search for the
amino acid sequence of the photosystem II protein D1 (PsbA). As there are usually a
large number of matches found we will use Entrez Boolean search features to restrict the
matches and narrow the search to the respective sequence.
• Go to Entrez web site and choose Protein form the drop-down menu
• Enter the terms ‘photosystem II’ in the search field and click Go or hit Enter
• Click History to see the number of matches
• Repeat the search with the same terms but put them into quotes: “photosystem II”
• Click Preview to see the number of hits
• Go to Add Terms, choose Organism from the drop-down menu, type Arabidopsis
and click AND. Then click Preview to show the number of hits matching the new
criteria
• To limit the hits to the RefSeq database (which is GenBank’s annotated sequence
database) click on Limits and in the appearing window go to the most right menu.
Choose RefSeq and click Go
• Click on the correct link to show the database entry in FASTA format; note that
the RefSeq accession number starts with NP, which identifies the sequence as
curated protein sequence.
• Use the display menu to show the entry in different formats
• Try a similar search for the nucleotide sequence; note that the gene name is
different from the protein name
• Try to find the entry with the shortest sequence
Now we will use the Entrez Gene database to search for information on the psbA gene.
Entrez Gene provides lots of information on genes and proteins based on the known
location of the genes on chromosomes that have been sequenced.
• Go the NCBI home page and choose Gene from the drop-down menu. Type
‘photosystem II protein D1’ and click Go.
• Limit the matches to Arabidopsis using the Preview section as before. Click on
the number shown at the right of the top row in the Most Recent Queries area.
• Select the correct link.
• In the appearing window, collect as much information as you wish.
Contact Jitendra Narayan
|
|
