X-Git-Url: https://bilbo.iut-bm.univ-fcomte.fr/and/gitweb/chloroplast13.git/blobdiff_plain/f8689d1f199221556dc52e80c5237c45addb0218..1e61bcbdaedf0f72f05c3dd365fc11d3a2071330:/annotated.tex?ds=inline

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-The field of genome annotation pays a lot of attentions where the ability to collect and analysis genomical data can provide strong indicators for the study of life\cite{Eisen2007}. Four of genome annotation centers (such as, \textit{NCBI\cite{Sayers01012011}, Dogma \cite{RDogma}, cpBase \cite{de2002comparative}, CpGAVAS \cite{liu2012cpgavas}, and CEGMA\cite{parra2007cegma}}) present various types of annotation tools (\emph{i.e.} cost-effective sequencing methods\cite{Bakke2009}) on different annotation levels. Generally, previous studies used one of three methods for gene finding in annotated genome using these centers: \textit{alignment-based, composition based, or combination of both\cite{parra2007cegma}}. The alignment-based method is used when we try to predict a coding gene (\emph{i.e.}. genes that produce proteins) by aligning DNA sequence of gene to the protein of cDNA sequence of homology\cite{parra2007cegma}. This approach also is used in GeneWise\cite{birney2004genewise}. Composition-based method (known as \textit{ab initio}) is based on a probabilistic model of gene structure to find genes according to the gene value probability (GeneID\cite{parra2000geneid}). In this section, we consider a new method of finding core genes from large amount of chloroplast genomes, as a solution of the problem resulting from the method stated in section two. This method is based on extracting gene features. A general overview of the system is illustrated in Figure \ref{Fig1}.\\
+The  field of genome  annotation pays  a lot  of attentions  where the
+ability  to collect  and analysis  genomical data  can  provide strong
+indicators  for  the study  of  life\cite{Eisen2007}.  Four of  genome
+annotation   centers   (such  as,   \textit{NCBI\cite{Sayers01012011},
+Dogma       \cite{RDogma},       cpBase      \cite{de2002comparative},
+CpGAVAS    \cite{liu2012cpgavas},   and   CEGMA\cite{parra2007cegma}})
+present various types  of annotation tools (\emph{i.e.} cost-effective
+sequencing    methods\cite{Bakke2009})    on   different    annotation
+levels. Generally, previous studies used one of three methods for gene
+finding       in        annotated       genome       using       these
+centers: \textit{alignment-based, composition based, or combination of
+both\cite{parra2007cegma}}. The alignment-based method is used when we
+try  to  predict  a  coding  gene  (\emph{i.e.}.  genes  that  produce
+proteins)  by aligning DNA  sequence of  gene to  the protein  of cDNA
+sequence of homology\cite{parra2007cegma}.  This approach also is used
+in GeneWise\cite{birney2004genewise}.  Composition-based method (known
+as  \textit{ab initio})  is based  on  a probabilistic  model of  gene
+structure  to  find genes  according  to  the  gene value  probability
+(GeneID\cite{parra2000geneid}).  In this  section, we  consider  a new
+method of finding core genes from large amount of chloroplast genomes,
+as  a solution  of the  problem resulting  from the  method  stated in
+section  two. This  method is  based  on extracting  gene features.  A
+general overview of the system is illustrated in Figure \ref{Fig1}.\\
 
 \begin{figure}[H]  
   \centering