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\begin{document}

%\title{T6}
%\author MM
%\maketitle


\chapter{Tag 6}
%\begin{itemize}
	\section{Aufgabe 6.1}
	
		\begin{figure}[ht]
		\centering
			\includegraphics[width=1.2\textwidth]{screenshots/t6/eps/snapshot1.eps}
		
			\caption{}
			\label{}
		\end{figure}
	\section{Aufgabe 6.2}	
\begin{figure}[ht]
	        \centering
		\subfloat[]{\label{fig:}\includegraphics[width=\textwidth]{screenshots/t6/eps/snapshot2.eps}}
		
		\subfloat[]{\label{fig:}\includegraphics[width=\textwidth]{screenshots/t6/eps/snapshot3.eps}}
		\caption{}
		\label{}
	\end{figure}

		
	\section{Aufgabe 6.3}
	There are 197 nucleotide sequences. 
        \begin{figure}[ht]
	        \centering
		\subfloat[]{\label{fig:}\includegraphics[width=\textwidth]{screenshots/t6/eps/snapshot4.eps}}
		
		\subfloat[]{\label{fig:}\includegraphics[width=\textwidth]{screenshots/t6/eps/snapshot5.eps}}
		\caption{}
		\label{}
	\end{figure}

	

\section{Aufgabe 6.4}
	Cytochrome b is one of the cytochromes involved in the electron transport in the respiratory chain of mitochondria. It contains eight transmembrane helices connected by intramembrane or extramembrane domains. It is the only cytochrome coded by mitochondrial DNA.	
	
		\begin{figure}[ht]
		\centering
			\includegraphics[width=0.7\textwidth]{screenshots/t6/eps/snapshot6.eps}
		
			\caption{}
			\label{}
		\end{figure}
		
\section{Aufgabe 6.5} 
	woolly mammoth 33,000 year-old. 
 \section{Aufgabe 6.6}
 	This DNA entry contain 1137 bp.
\ section{Aufgabe 6.7}
	The deduced protein means that the sequence was not found with an experimantal techniques(for example  with X-ray crysallography or NMR spectroscopy), bt was predicted by some structure prediction programms.

	
		\begin{figure}[ht]
		%\centering
			\includegraphics{screenshots/t6/eps/snapshot7.eps}
		
			\caption{}
			\label{}
		\end{figure}
	\section{Aufgabe 6.8}
 	The cytochrome B contains  378 aa.
\ section{Aufgabe 1}
	Noe there were 27 sequences found.
	
		\begin{center}
			\begin{figure}[htbp]
			%\centering	
				\includegraphics{screenshots/t6/eps/snapshot8.eps}
				\caption{}
	        	        \label{}
			\end{figure}
		\end{center}
		ORGANISM  Aedes aegypti
              Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota;
              Neoptera; Endopterygota; Diptera; Nematocera; Culicoidea;
              Culicidae; Culicinae; Culicini; Aedes; Stegomyia.


\section{Aufgabe 2} 
	There are 1735 bp .

	
		\begin{figure}[htbp]
		\centering
			\includegraphics{screenshots/t6/eps/snapshot9.eps}
		
			\caption{}
			\label{}
 		\end{figure}
	\section{Aufgabe 3}
 	There are 563 aa. 
   \section{Aufgabe 4}
	The first five amino acids of the apyrase enzyme sequence:
	\begin{itemize}
	\item Methinine
	\item Adenin
	\item Glycine
	\item Arginine
	\item Proline
	\end{itemize}	
\section{Aufgabe 5}
 	The mRNA for this enzyme was found in the tissue type called "salivary gland".
\ section{Aufgabe 6}
	Hematophagy habit of certain animals of feeding on blood. Since blood is a fluid tissue rich in nutritious proteins and lipids that can be taken without enormous effort, hematophagy has evolved as a preferred form of feeding in many small animals such as worms and arthropods. The hemostasis is the stoppage of bleeding after the mammal organism has been biten.
	\begin{figure}[ht]
		\centering
		\subfloat[]{\label{fig:}\includegraphics[width=0.4\textwidth]{screenshots/t6/eps/snapshot10.eps}}\qquad
		\subfloat[]{\label{fig:}\includegraphics[width=0.4\textwidth]{screenshots/t6/eps/snapshot11.eps}}\quad
		\subfloat[]{\label{fig:}\includegraphics[width=0.4\textwidth]{screenshots/t6/eps/snapshot12.eps}}\qquad
		\subfloat[]{\label{fig:}\includegraphics[width=0.4\textwidth]{screenshots/t6/eps/snapshot13.eps}}\quad
		\subfloat[]{\label{fig:}\includegraphics[width=0.4\textwidth]{screenshots/t6/eps/snapshot14.eps}}\qquad
		\subfloat[]{\label{fig:}\includegraphics[width=0.4\textwidth]{screenshots/t6/eps/snapshot15.eps}}\quad
		\subfloat[]{\label{fig:}\includegraphics[width=0.4\textwidth]{screenshots/t6/eps/snapshot16.eps}}\qquad
		\subfloat[]{\label{fig:}\includegraphics[width=0.4\textwidth]{screenshots/t6/eps/snapshot17.eps}}\quad
		\subfloat[]{\label{fig:}\includegraphics[width=0.4\textwidth]{screenshots/t6/eps/snapshot18.eps}}\qquad
		\subfloat[]{\label{fig:}\includegraphics[width=0.4\textwidth]{screenshots/t6/eps/snapshot19.eps}}\quad
		\caption{}
		\label{}
	\end{figure}
\section{Aufgabe 6}
	The term "apyrase"  was fisrt reporded in print by O. Meyerhof in 1945.
\section{Aufgabe 7}
	The authors feeded the Aedes aegypti organisms that they reared with sugar and blood solution.
\section{Aufgabe 8}
%\end{itemize}
\section{Aufgabe 9}
	The amino acid sequence of mosquito apyrase  was compared with the human placental and rat liver amino acid sequences.
\section {Aufgabe  6.1: BRCA1}
%	\begin{enumerate}
		\subsection{} There were suggested in some studies, that the people carriers of the BRCA1 gene may have an increased risk of:
			\begin{itemize}
				\item Ovarian Cancer,
				\item Papillary Serous Carcinoma of the Peritoneum (PSCP), 
				\item Prostate Cancer
			\end{itemize}
		\subsection{} UniProtKB/Swiss-Prot found 20 interactions, string server showed 11 interactions.
			\begin{figure}[ht]
				\centering
				\subfloat[]{\label{fig:}\includegraphics[width=0.4\textwidth]{screenshots/t6/eps/snapshot23.eps}}\qquad
				\subfloat[]{\label{fig:}\includegraphics[width=0.4\textwidth]{screenshots/t6/eps/snapshot22.eps}}\quad
				\subfloat[]{\label{fig:}\includegraphics[width=0.4\textwidth]{screenshots/t6/eps/snapshot21.eps}}
	        		\caption{}
			        \label{}
	        	\end{figure}
		%\item 
			

		\subsection{} 
		\begin{itemize}
		\item
		The quality score is inversely proportional to the average cost of all pairs of mutations oberved in a particular column of the alignment - a high alignment quality score for a column would suggest that there are no mutations, or most mutations observed are favourable. A good alignment would have no gaps at all. In clustal we were using one  weight matrix, and one set of penalties for all the sequences. The best set of parameters for one part of the alignment may not be the best for another part. The possibility of makeing a choose here could be a  stpe towards improving the quality of our alignment.
		\item
		The cost of mutations in sequence alignments are controlled by substitution matrices. In our case it was worth changing from BLOSUM to PAM, cause we quality was better and the gaps in more poorly related regions has vanished. Anyway the decision about changing the matrix is individual and depends on what we want to do. If we looking for, for example, domains and highly conserved regions we would better work with blosum.

			\begin{figure}[ht]
				%\centering
				\subfloat[]{\label{fig:}\includegraphics[width=0.3\textwidth]{screenshots/t6/eps/snapshot24.eps}}\quad
				\subfloat[]{\label{fig:}\includegraphics[width=0.3\textwidth]{screenshots/t6/eps/snapshot26.eps}}\quad
				\subfloat[]{\label{fig:}\includegraphics[width=0.3\textwidth]{screenshots/t6/eps/snapshot_pam28.eps}}
	        		\caption{}
			        \label{}
	        	\end{figure}
		\item Gap-opening penalties (GOP) control the cost of opening gaps in our alignment. The higher the value, the more difficult it is to insert a gap in the alignment. The gap-opening penalty is applied once for the opening of each gap. We can see the effect of tuning it in a Fig. 6.x. 
	Gap-extension penalties controls the size of each gap. The lower the value, the easier is is to end a gap. 	
			\begin{figure}[ht]
				\centering
				\subfloat[]{\label{fig:}\includegraphics{screenshots/t6/eps/snapshot_gop030.eps}}\qquad
				\subfloat[]{\label{fig:}\includegraphics{screenshots/t6/eps/snapshot_gop10029.eps}}\quad
	        		\caption{}
			        \label{}
	        	\end{figure}
\end{itemize}
%\end{enumerate}
Clustal is optimized to align sets of sequences that are
entirely colinear, i.e. sequences that have the same
protein domains, in the same order.
\end{document}