Suppose I have sequenced one of my clones, how can I know which regions constitute the exon, intron, splice sites, splice variants, signal peptides and disufide bridges? What is the easiest method for getting the translated nucleotide sequence, and how to predict the secondary structure of the translated protein sequence in groups? I also want to know how SignalP software works.
Intron exon junctions a relatively well conserved when it comes to nucleotide sequence. You maybe able to find your sequence on one of the database such Ensembl, Entrez or NCBI, the genomic DNA if present will have the exon intron maps splice sites and much more. However, if your looking to express your protein you would be better of generating the clones from cDNA.
With regard to signal sequences, though there is little amino acid homology between them there basic structure is the same, Positively charged amino terminus, hydrophobic core followed by small aploar residues.
Finally, when it comes to structure your best bet is to find a similar protein (functionally) ie if it is a calcium channel use a calcium channel that has been mapped as a template for your protein. There are various programs on the net that will do this for you.
Thanks Jason. It will be helpful. I'll get to you once I have tried myself. At present I have a doubt as to what does 5'3' and 3'5' frame 1,2,3 mean in expasy tool. I tried translating my sequence in it and I got the protein sequence in frames.
Whether for working with FGENESH any license is required or we can use the crack version ........I mean ethically?
My question is whether for working with Ensemble, Expassy, FGENESH, SignalP, GENSCAN, does licensed versions are required for the same
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