Hello everyone,
I was wondering what kinds of information can be deduced from a gene's sequence?
I am studying Biology and was assigned a Bioinformatics task for my Molecular Biology project on a gene of the Baculoviridae virus - which is a DNA binding protein. I decided to gather the sequences of many strains and created a sequence alignment from it.
However, now I am stuck. My professor says I could look at the amino acids and try to determine which regions are possible active sites, which regions a possible DNA binding regions etc. How do I determine this?
I have attached a photo below of the sequence alignment of alpha, beta, gama, and delta Baculoviridae.
Thank you
I would recommend you first check your nucleotide chromatograms first. Did you get the amino acid sequenced or was the nucleotide translated to amino acid and aligned? If this is the same gene, there is way too much variability it seems. At genus level and also at species, you can track the exact nucleotide which changed that led to change of the amino acid and it become a different species. You can also make secondary structure from this and see if the protein holding is changing at any point due to change in amino acid. What question are you trying to address?
Go to the protein databases. It will show you the regions of the gene marked as active regions from reference sequences deposited. You can also see the domains of the protein. Compare the domains of your sequence with that of the reference and see what you get.
You need to decide whether you want to use a consensus sequence derived from your alignment or if you just want to use one representative sequence.
You can go to Expasy to find a whole bunch of tools for characterising protein sequences. One of the most popular ones is PROSITE, where you can upload your sequence in fasta form and it will scan databases and give you the information you are looking for. They have examples so that you can see the format they require.
https://prosite.expasy.org/
https://www.expasy.org/vg/index/Protein
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