Alot of ngs data has been analysed, but i want to ask what is the criteria for identifying a certain gene in a newly sequenced genome is new?
I really have no clue what you mean. But my best guess is that you ask for criteria for annotating a new gene in a new assembled genome. Long story short: look for start and stop codons in appropriate orderings. Having cpg islands and all the other possible marker sequence motifs. Also RNA-seq experiments can be quite useful.
You can identify new genes by (i) similarity to orthologs in related organisms; (ii) finding certain 'signals' that mark a gene (start and stop codons, promoter motifs, etc); (iii) by analyzing the 'content' of encoded proteins, i.e. statistics specific to coding regions. Look for 'gene finding' reviews in PubMed, most of them are from the 1990s but little has changed in this field.
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