GeneSeqer Detective

AtGDB Gene Structure Annotation: How-To

As you progress, you may find some of the information or instructions confusing.
At any time you may go back and review the vocabulary.

STEP 1: Find a DNA sequence.

In order to begin using this service you must first have a DNA sequence. Now, if you are a researcher you would be discovering your own DNA sequences that you are interested in. However, since most using this site are not current researchers, someone who IS currently doing research has provided a list of DNA sequences that they are interested in and that they think may prove to be interesting. Say 'thank you' to Dr. Volker Brendel's research group at Iowa State University.

When choosing a sequence it is important to choose sequences of less than about 30,000 base pairs. The GeneSeqer program will take roughly one half hour to perform a search on a sequence of about 60,000 base pairs. Use this as a guide so that your search can be done in a timely manner. Please choose a DNA sequence from the drop down list of sequences below to run on the GeneSeqer program.





Show All Entries Show 20 Random Entries/List

STEP 2: Enter your DNA sequence.

Now that we have a DNA sequence that we are interested in we need to enter it into the GeneSeqer program. There are a number of ways to enter a DNA sequence. You may enter each nitrogen base by hand, or even upload a file containing the sequence in it. However, the easiest way to enter your DNA sequence is by entering the GenBank accession number. To do this simply choose the GenBank format button and type the accession number in the appropriate box. Be sure to enter it exactly as it appears, small mistakes will result in failure of the search or searching with the wrong DNA sequence.

Paste your genomic DNA sequence here:

... or type in the GenBank accession number of your sequence:
Select format: plain FASTA GenBank
Sequence name: (optional, used in plain sequence format only)
From position: to position: Strand: original reverse both


The above 'position' indicator allows you to tell the program to only look for matches to certain segments of your DNA fragment. For instance, you may want to look for matches of the segment starting with base pair 510 and ending with base pair 12425. This is also a way to shorten a lengthy DNA fragment. To search the entire sequence just leave this area blank.

You may also choose to only search in one direction along your sequence for potential matches. The program will automatically look in both directions of DNA unless you specify otherwise. Therefore, unless you would like this changed, simply leave the 'both' button selected for you search.

STEP 3: Selecting cDNA/EST sequences.

This step allows you to choose which types of previously sequenced DNA (cDNAs & ESTs) you would like to compare to your sequence. For an initial search we are going to select the TUG button in the 'All Plants' category. This sequence collection represents the Tentative Unique Gene (TUG) clusters assembled using the PlantGDB contiging method. Generally, when characterizing a large genomic sequence, the detection of genic regions is the primary goal. Only after their detection, are these regions looked at in greater detail.

Spliced Alignment: The output of this selection will show an optimal threading of a significantly matching cDNA/EST sequence to your DNA by aligning putative exons (thick bars) only and displaying putative introns (thin bars) as (long) gaps in the cDNA/EST.

Database EST TUG cDNA
Shortcut
All Plants
All Monocots
All Dicots
All Grasses
Arabidopsis thaliana
Avena sativa
Beta vulgaris subsp. vulgaris
Glycine max
Gossypium arboreum
Gossypium hirsutum
Hordeum vulgare
Lotus japonicus
Lycopersicon esculentum
Lycopersicon hirsutum
Lycopersicon pennellii
Marchantia polymorpha
Medicago sativa
Medicago truncatula
Mesembryanthemum crystallinum
Oryza sativa
Pinus taeda
Populus tremula X Populus tremuloides
Secale cereale
Solanum tuberosum
Sorghum bicolor
Sorghum propinquum
Triticum aestivum
Zea mays
Database EST TUG cDNA

STEP 4: Select a splice site model

This step is simply to pick the species that is most closely related to the DNA sequence you are interested in.

STEP 4: Select splice site model

Species (selects species-specific splice site model)

STEP 5: Submit your DNA sequence for comparison.

Once all of the steps have been completed you are now ready to submit your sequence to GeneSeqer for comparison with the database. If you have an unusually large sequence you may want to have the output sent to an e-mail address, otherwise it will be sent to your browser. Your browser will automatically refresh until all of the output is on your screen.

STEP 5: Submit job

Send the output to this email address:
HTML formatted output [default: simple text].This option will not work if your mailer wraps long lines.

<<-- Don't forget to send it to GeneSeqer!!


STEP 6: Interpreting Results

When you receive your output from GeneSeqer you will then have the job of interpreting what it all means. You are encouraged to browse around your results and see what you can make of them. If you need some guidance in deciphering all of that information please go to the interpreting results page which will assist you.

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