What software can do?

For the first time when I had to implement sequence analysis it was three years from now. The subject was HIV-1 As I was very poor at that time I had no money for good computer and all of the work I needed to do I performed on PC 486 with Windows 3.1. That was a disaster, because I couldn't install any program for sequence analysis which would be simple and usable, because there were some programs for DOS and WIN 3.1, but I couldn't use any of them. Their interfaces were bad and commands were rather linked to Q-basic than genetics. First of all I wished to construct genetic map of HIV-1 to see where in genome some genes are located. I took list of paper, drow long line and have started to mark positions of structural and functional genes. After three hours I have decided to stop with such a trivial work. There was no genetic map, there was something from which I couldn't deduce what it is, although I have constructed that. But, I told to myself, if I am bad painter, that doesn't mean that I cannot perform restriction analysis by myself. I have decided to bravely step in such a process. I left my home and have gone to one Internet caffe to find list of restriction endonucleases available on the net. I have found 50 enzymes, and when I came home, I wrote a table with those enzymes, marked their names, source and sites of restriction. I was happy, but that wasn't enough. I had to go to library on their computer to use printer, and after two days I get my first list of restriction nucleases. I took HIV-1 gene sequence, printed on 10 papers, then I took list of restriction endonucleases and have started with the analysis. Genome of the HIV-1 is composed from 9181 bp, and I had 36 hours to find just 11 restriction fragments, after what period I gave up. In that time, I had a difficult debate with my good friend, doctor of human genetics, who told me that Prusiner was absolutely right when he described prion as independent infectious agent without nucleic acids. My friend claimed that the fact because of Prusiner won Nobel prize is enough to brake down central dogma of molecular biology. "Genetics has fallen in water" she said for several times. One day I came to her on our debate, she gave me on our last meeting many questions about prions and prion diseases on which I needed to answer, and one of them was: "How it could be possible that prion has no nucleic acids and that ic could evolve without them?". For her that was an evidence that some living being could exist without nucleic acids, and that when I become doctor of genetics, that field wouldn't exist. I have answered on her question that it isn't possible that prion haven't evolved from nucleic acids, but I couldn't prove that. I told her that we can take amino acid sequence of infectious prions found in human and perform backtranslation, then we can isolate sequence that is most probable and compare it with sequences in human genome. It was impossible for me to do that by myself, I needed strong computer and good program for that.

Today, the situation is different. If I would like to performed backtranslation and then FASTA or BLAST analysis by myself, I wouldn't succeed in whole eternity. But, now I can do that in few minutes. The situation on prions is also different. Apparently I was right and my friend was wrong, because it was proven that prions evolve from nucleic acids, although remains unclear why nucleic acids cannot be seen in protein structure. In front of me I have constructed map of HIV and many other genome sequences and I can perform any analysisi I wish, except I cannot search for novel sequences in genome or prepare expression experiments. For that I will need a laboratory. But, with this program, Vector NTI Suite 8.0, produced by Informarxinc, I can do:

* construct genetic maps
* manipulate sequences
* preform restriction analysis wit 229 enzymes (and add new ones)
* perform RFLP analysis
* create my own database
* find ORFs with specified length and genetic code (17 different codes)
* Perform translation and backtranslation with specified genetic code
* Perform e-PCR analysis, find and construct primers
* Perform FASTA and BLAST through Internet connection
* Perform gel tests; polyacrylamide gel, agarose gel, PFGE
* Align nucleic and aminoacid sequences
* Perform blocker analysis in process of gene reconstruction
* Sequence assembling
* Visualization and processing of PDB files
* Direct access to PDB database
* Perform many protein analysis; amino acid composition, hydrophobicity, charge, etc.
* Analysis of microarray files
* And more other functions

When I started to use computer and software for sequence analysis I have fallen from world of theory in world of experiments. All my projects till now were theoretical because I had no possibilities to prove my ideas on the experimental level. But, with this program I can prove my ideas. My current project is linked to evolution and regulation of LINE-1 transpozones in eukaryotes. I have analyzed Xq28 region of human genome, and Xp region of chimpanzee which is still in process of sequencing. In both, humans and chimpanzee I have found LINE-1 gene fragments, which were identified by high value of identity by FASTA. There are 25 sequences now assigned in NCBI TPA database, and through further analysis I an expecting to get answer on one pretty important question - are LINE-1 transposones really highly regulated in genome of eucaryotes? To prove that I would have just access to NCBI database, which I already have, and knowledge to use mentioned software and interpret results of implemented analyses.

The genetics is very comfortable scientific field, because one can reveal secret of life from just one cell of an organism. The computational genetics makes possible to make experimental laboratory in one's home.