I'm a computer scientist who is starting to dabble with biology. My eventual goal is to model different kinds of cells with a computer program. As of right now, I'm just trying to take some smaller steps.
First, I downloaded a complete human genome from http://hgdownload.cse.ucsc.edu/downloads.html#human There is a FASTA file for each chromosome.
Then, I wrote a java program which can convert FASTA DNA sequences into the appropriate amino acid chain.
Next, I made my program look for the "start" code (ATG) and "stop" codes (TAA, TAG, TGA).
So, now I have sequences of amino acids which might theoretically end up folding into proteins. But, before I start diving into protein folding, I wanted to try to verify that the steps I took so far were done correctly. I looked up some important human genes in an online database and found their amino acid sequences. I then searched through my program's data for those sequences and confirmed that they were there. However, the gene was in a different base-pair location than the database said that it should be in.
This led me to some questions, which, so far I have been unable to answer and hopefully people here will be able to help shed some light.
I know there are a lot of different publicly available genomes. Maybe the UCSC one that I downloaded is different from the one used by the gene database. How much does each genome vary from each other genome and in what ways do they vary?
In attempting to answer that first question, I was going to download a bunch of genomes from the 1000genomes website and do some comparisons, but I wasn't sure which files to download. Each of the files begins with either ERR or SRR and I'm not sure what that means. This is the folder I'm currently looking in ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/data/HG00239/sequence_read/
Lets say I'm trying to model a white blood cell. How do I know which parts of the genome get turned into proteins for that type of cell?
Sorry if anything I said doesn't make sense. As I said, my expertise lies in programming, not biology/genetics.