I have a problem with defining pseudogenes in bacteria genome. I defined pseudogene as an another copy of gene in genome.
Because my genome is bacteria I don't have any introns, so every same annotation for one gene will be an extra copy - pseudogene. I have 2000 unique genes and 454 repeated at least once. Going this way I found around 1000 pseudogenes. In comparison to other related species this amount is huge - that's why I am suspicious about my results.
So my questions are:
*Which one of defined pseudogenes represent gene and have functionality? How can I find them?
*This may be a stupid question but: Is it possible to have two same annotated genes divided by nucleotides in bacteria genome (one next to another with break)? If yes, is it one gene or gene and its pseudogene? Example below:
gene A_1-AGTCTATGTA-gene A_2
Many thanks for any suggestion.