As par of my research work, I have to deal with the expression patterns of certain genes. I came across different sequences for same genes in different publications. So can anyone please suggest me a program which can be used to check whether a particular gene sequence is working or not? Also if possible can anyone please mention me the steps for using it?
Dear Abdilash,
Could you please be a little more specific? What do you mean by "whether a particular gene sequence is working or not?"?
Is your concern about the gene expression? The mRNA translation?
There are many needed feature for "a gene to work", such as a promoter, a terminator, a start codon, a ribosome binding site...
We need more information on your need.
Dear Abdilash,
Could you please be a little more specific? What do you mean by "whether a particular gene sequence is working or not?"?
Is your concern about the gene expression? The mRNA translation?
There are many needed feature for "a gene to work", such as a promoter, a terminator, a start codon, a ribosome binding site...
We need more information on your need.
There is also a further problem with the question
Genes are not the same in all individuals even of the same species. This may be due to selection, drift or mutation. Some of the mutations may increase translation or decrease it. Gene expression (RNA) data alone is probably insufficient to say whether a gene is or is not translated. Of course the genes you are interested in may not be translated in which case translation may not be relevant. Genes in that latter category include the tRNAs. rRNAs etc.
There is also the problem of incorrect annotation. In some eukaryotes gene models may be incorrect in up to 30%. This is before taking alternative splicing into account.
I suspect that there is no single programme that will answer all your questions but we may be able to assist you further if a little more information is provided - for example are the genes prokaryotic or eukaryotic, are the genes translated, are the genes from a single species etc.
Dear Thibault Caradec and David Mitchell.....Thank you very much for the suggestions.
Actually I have to deal with the mRNA expression patterns of genes from rats (Reverse transcriptase PCR). A few among them include L-FABP, H-FABP, GLUT-1, AQP-9.......
The rat genome is reasonably well annotated. At least the coding sequences are. There are lots of problems with identifying enhancers, promoters, transcription start sites etc. This is not a problem unique to rats: it is a problem for all eukaryotes.
I do not think that there is one simple (or not so simple) programme that will solve your problem. if there was I think everyone would be using it. While the software for finding coding sequences in well studied eukaryotes is reasonable good, locating the non coding elements that affect transcription is a problem that a lot of people have been struggling with for a long time. I wrote a programme some time ago - a variable Markov order Gibbs sampler - for a similar problem but then we had some idea where to locate the common sequences. I am not sure if it would be of much use locating promoters let alone enhancers and other elements.
I will think a bit more on this question but I suspect that you are working at the boundaries of current knowledge and the answering this question might be difficult.
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