Download 1 - Cal Poly

1.) Open your Web Browser such as Internet Explorer and type in the following address
http://www.ncbi.nlm.nih.gov
To Search for information on DNA you have sequenced
1.) From the above website choose BLAST which is in the toolbar above the search box.
2.) You will then need to choose the appropriate databases to search depending on what
type of DNA you have sequenced. (ie, genomic, translated proteins, etc) In this example
I have chosen to search the nucleotide-nucleotide (blastn)
3.) Once you have chosen your database you will be given search options.
4.) Copy your DNA sequence and Paste it into the Search box.
5.) Choose your appropriate database (nr will search all databases)
6.) Hit BLAST!
7.) Your search is put into a queue and estimated time is given for the completed search.
8.) Hit Format! to see your results
9.) A list of results will be given with a score and E value to show how close your
sequence was to the blast results.
10.) Click on the link of your results for a detailed description.
Finding the physical location of your gene
1.)Return the www.ncbi.nlm.nih.gov homepage and follow the Map Viewer option
under the Hot Spots. This will lead you to http://www.ncbi.nlm.nih.gov/mapview/
2) Either select your organism of choice (eg. S. cerevisiae) from the search pull down
menu or click on the name of the organism in the phylogenetic tree. If you are looking
for a specific gene you can type the name of it in the search box to the right of the pull
down menu (eg. act1).
3) This will lead you to a map of the chromosomes of the organism.
4) If you searched for a specific gene, a red mark will appear next to any chromosomes
which contain a matching gene. Click on this chromosome or other chromosome of
interest to view physical location. Or click on gene under search results corresponding to
the gene of interest.
5) Zoom out too see surrounding genes.
6) Click on gene of interest (ACT1) for more information.
Finding a gene in the human genome
1) Follow instructions above to get to map viewer. www.ncbi.nlm.nih.gov/mapview/
ALDH2
hbb
cftr
dmd
eg. arabidopsis formate dehydrogenase
click on chromosome with gene of choice or on map element link corresponding to gene
of choice.
click on TAIR for more information
to retrieve sequence: scroll down to nucleotide sequence. select data you are interested
in.
for enzymatic pathway information: click tools at top of screen
select AraCycPathways
too see the entire metabolic map click metabolic map
too see pathway involving a specific enzyme click main Query Page
enter protein of interest in the query by name entry field
eg. formate dehydrogenase
select reaction of choice
select the in pathway link
moving the mouse across the blue lines will give you information about the reaction.
moving the mouse across the red text will give you more information about the
compound in the lower left corner of the page.