Hi Hassan,
gene knockout means gene deletion from the chromosome. Regarding the best protocol it depends on what are you planing to use it for. gene deletion could be done in bacteria, mammals, insects, etc. there is a new technology you might want to read about called CRISPER9. Hope that helps.
In genetics, a deletion (also called gene deletion, deficiency, or deletion mutation) (sign: Δ) is a mutation (a genetic aberration) in which a part of a chromosome or a sequence of DNA is lost during DNA replication. Any number of nucleotidescan be deleted, from a single base to an entire piece of chromosome.The smallest single base deletion mutations are believed to occur by a single base flipping in the template DNA, followed by template DNA strand slippage, within the DNA polymerase active site. Deletions can be caused by errors in chromosomal crossover during meiosis, which causes several serious genetic diseases. Deletions that do not occur in multiples of three bases can cause a frame shift by changing the 3-nucleotide protein reading frame of the genetic sequence. For detecting, please see below reference. (From Wikipedia)
Shmilovici, A.; Ben-Gal, I. (2007). "Using a VOM Model for Reconstructing Potential Coding Regions in EST Sequences". Journal of Computational Statistics. 22 (1): 49–69. doi:10.1007/s00180-007-0021-8.
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