Frequently Asked Questions
- What is a synthetic gene?
A synthetic gene is a DNA molecule artificially constructed using a set of oligonucleotides without a physical DNA template. Currently, our database focuses on those synthetic genes that have been re-designed to improve protein over-expression.
- What is the difference between site-directed mutagenesis and gene synthesis?
Although both methods can introduce mutations, site-directed mutagenesis requires a physical DNA template whereas gene synthesis does not.
- Why do people re-design a gene?
Roughly two reasons: 1) To boost protein expression; 2) To study the function of the protein. However, currently, our database does NOT collect mutant genes for the latter purpose.
- Why do people synthesize a gene?
Gene synthesis can introduce any number of mutations (mainly silent), therefore, it is ideal for gene re-design experiment.
- Why are synthetic genes useful?
1) They form an important reference data set to guide synthetic gene design in the future; 2) They serve as a good training set for bioinformaticians to derive rules governing protein translation and function.
- Why should we build a new database?
Many synthetic genes (>60%) have only been reported in publications ~ never submitted to GenBank or other online resources
- Is SGDB different from RECODE?
Yes. RECODE is a database that collates only naturally occurring recoding events such as frame-shifting, bypassing (hopping) and stop codon redefinition. Our SGDB collects artificially re-designed genes.
- How often is the SGDB updated?
Once a user submits into our database, it will be automatically updated. Therefore, it depends on how often a new record is submitted.
- How can I submit a synthetic gene?
You need to follow these three steps in order: 1) Submit the publication that reported the gene; 2) Choose this publication, submit the sequence of the natural gene; 3) Then for this natural gene, submit your synthetic genes. To do this, you need to register an account with a valid email first.
- How can I update a record that I submitted before?
Simply go to http://www.evolvingcode.net/codon/sgdb/update.php. After you log in, select which you want to update: publication, natural genes or synthetic genes? Under each category, select the record needs to be updated from the list. Then change the specific field in the update form, which will be similar to the submission form.
- Does the synthetic gene code exactly the same protein as it natural counterpart?
Not always. It is very often to see several amino acid substitutions in the synthetic genes due to introduction of restriction sites and other reasons.
- What is the sequence comparison tool?
This tool is created for aligning the synthetic gene and the natural gene so we can view the base substitutions and codon usage differences at each codon position. It will allow users to identify the rare codon clusters. To use it, users can define codon fitness according to various criteria. Users can copy and paste their own genes into the two boxes to compare (i.e., they are not necessarily from our database) as well.
- Do I need to create a user account?
Not necessarily. The account is only used for those who plan to submit/update records into our database. The browsing of content in this site is totally free and requires no user account.
- I have some synthetic genes, but these genes do not express better than the natural gene. Unfortunately, negative results usually don't get published. Can I submit them into this datbase?
Sorry to hear about that. We totally understand this situation. Although currently our database only collect those sequences having published data, we are still seeking a way to include those re-designed synthetic genes into our database provided that these sequences do have experimental data. Let us know if you have the similar problem. And we will notify you once we have a solution to this.
- How can I download all XML files for the SGDB?
Currently, we have dumped all XML files into the directory http://www.evolvingcode.net/codon/sgdb/tmp/. You can also find a zip file that contains all XML files. These files will be updated frequently if there are many new additions into the database.
- Where is the XML schema located?
It is at http://www.evolvingcode.net/codon/sgdb/sgdb.xsd.
- Who should I contact if I still have questions?
Please contact Gang Wu or post a message at our support forum.