+In previous section, extracting core genes based on NCBI annotation caused some lost of genes due to annotation process of NCBI. Annotation tool play an important role for this losts, because it represents the first stage of gene identification. Good annotation tool still be challenged subject. (Genis Parra in 2007) published a paper state that the subject of accurately genomic and/or gene annotation is still an open source problem, even in the best case scenario where any project has all the expert biologists resources to annotate gene structures, the catalogues of genes can still unclear and still less accurate than experts. \cite{Bakke2009} also stated ("Errors in the annotations are routinely deposited in databases such as NCBI and used to validate subsequent annotation errors."). So, good core genes still need good annotation tool. A lot of softwares today’s were developed for extracted core genes for eukaryote and prokaryote organisms such as CEGMA\cite{parra2007cegma}, Coregenes 3.0\cite{zafar2002coregenes}, and Dogma\cite{RDogma}. The most appropriate annotation tool for chloroplast and mitochondrial genomes is Dogma.
+
+\subsubsection{Why Dogma rather than NCBI annotation?}
+Dogma is an annotation tool developed in the university of Texas by \cite{RDogma} in 2004. Dogma is an abbreviation of \textit{Dual Organellar GenoMe Annotator}\cite{RDogma} for plant chloroplast and animal mitochondrial genomes.
+It has its own database for translated the genome in all six reading frames by quering the amino acid sequence database using Blast\cite{altschul1990basic}(i.e Blastx) with various parameters, and to identify protein coding genes\cite{parra2007cegma,RDogma} in the input genome based on sequence similarity of genes in Dogma database, further more it can produce the \textit{Transfer RNAs (tRNA)}\cite{RDogma} and the \textit{Ribosomal RNAs (rRNA)}\cite{RDogma} and verifying their start and end positions rather than NCBI annotation tool.
+
+\subsubsection{Core genes based on Dogma Genes names and counts}
+The method for extracting core genes using Dogma annotation can be more reliable and confidence than NCBI. This is because NCBI annotation carry some annotation errors\cite{Bakke2009}. The method of extracting core genes can summerized in the following steps:\\
+
+\textbf{Step I: Annotate Genomes}\\
+
+In this step, we starts to annotate same chloroplast genome population, this method is done manually for 99 genomes. The output from Dogma annotation website is collection of coding genes file for each genome in GeneVision\cite{geneVision} file format.\\
+
+\textbf{Step two: Genes Defragmentation}
+As a result of the annotation from dogma is coding genes with fragments. It is not considered as gene duplication.
