As part of my research work, I have to check the expression of some genes. However when I go through references, I got different sequences for the same gene. I wish to know which of these sequences will be working or not. Can anyone please suggest me some useful software which can give an idea whether a particular sequence is working or not?
Blast from NIH is an excellent source. However, expression of a gene entails many more aspects than a wild type and correct sequence. In fact, often one can get far higher level of expression by a variety of deliberate and carefully crafted changes in gene sequence, such as codon optimization, which can increase gene expression as much as an order of magnitude or higher.
Hi Abhilash,
We usually use Blastn, when checking primer sequences or similar. Its free and you can choose the reference genome you need.
Best, Anja
Blast from NIH is an excellent source. However, expression of a gene entails many more aspects than a wild type and correct sequence. In fact, often one can get far higher level of expression by a variety of deliberate and carefully crafted changes in gene sequence, such as codon optimization, which can increase gene expression as much as an order of magnitude or higher.
- I agree with the above: you may have different sequences corresponding to different loci from the same gene but as long as you can verify they derive from the same gene by BLASTn then that is all that matters
- I will add a caveat: Different regions of the same gene might actually equate to different isoforms corresponding to different splice patterns; and these things are nearly always tissue specific
- Thus, make sure that you are not just dealing with the right gene but the correct isoform of that gene for your tissue sample. Once again Blast n will provide information on if your sequence derives from a particular splice variant
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