These parameters influence the alignment scoring similar to the same values in a standard alignment.
\begin{table}[H]
\begin{tabular}{llp{9cm}}
\hline
parameter & default & description\\\hline
-M, --matrix &- & The domain similarity matrix. This one needs to fit the data in the database (e.g. If you work with a database that contain Pfam domains, use the corresponding Pfam similarity matrix.\\
--gop & -50 &Gap opening costs\\
--gop & -50 & Gap opening costs\\
--gep & -10 & Gap extension costs\\
\hline
\end{tabular}
\end{table}
Gap opening costs are only taken into account when the gap occurs in the middle of a domain arrangement. Gaps at either end of a DA are assumed only penalized using the 'gap extension' costs.
\subsection{Data bases}
We provide a range of precomputed databases on our website. We currently provide databases based on the InterPro annotations. If you want to compute a database based on you own data you can do that very easily using the makeRadsDB program included.
We provide a range of precomputed databases on our website. We currently provide databases based on the InterPro annotations. If you want to compute a database based on you own data you can do that very easily using the makeRadsDB program included (see Section \ref{section:makeRadsDB}).
\subsection{Output format}
The output is in a very simple textfile format. The hits are listed in a table of five \emph{tab} separated columns. The first column contains the alignment score and the second the normalized version. The third column contains the the target id followed by the sequence length in the fourth column.
The output is in a very simple textfile format. The hits are listed in a table of five \emph{tab} separated columns. The first column contains the alignment score and the second the normalized version. The third column contains the the target id followed by the sequence length in the fourth column.
The table is sorted according to the first column.
...
...
@@ -90,7 +94,7 @@ The table is sorted according to the first column.
A program to compute a data base that can be used by RADS. A database consists of two files an index file (SQLite database) and an arrangement file (simple textfile) (e.g. if the name of the data base is MyDB the files needed are MyDB.db and MyDB.da).
A program to compute a data base that can be used by RADS. A database consists of two files an index file
(SQLite database) and an arrangement file (simple textfile) (e.g. if the name of the data base is MyDB the
files needed are MyDB.db and MyDB.da).
\subsection{Program options}
\subsubsection*{General options}
The basic options
\begin{table}[H]
\begin{tabular}{llp{9cm}}
\hline
parameter & default & description\\\hline
-h, --help & - & Produces this help message\\
-i, --input & - & Domain arrangement file(s) that should be turned into a database. \\
-I, --InterPro & - & Used to turn the InterPro annotation file (match\_complete.xml.gz) found on \url{https://www.ebi.ac.uk/interpro/download.html} into a RADS database. This option is used to compute the precomputed InterPro databases.\\
-s, --seqs & - & Sequence files. Are used in combination with the domain arrangement files. If none is given all sequence lengths are set to 0.\\
-o, --out & - & The output prefix used to produce two files in format prefix.db and prefix.da. Be aware that we currently do no support adding data to an existing data base.\\
-h, --help & - & Produces this help message\\
-i, --input & - & Domain arrangement file(s) that should be turned into a database. \\
-I, --InterPro & - & Used to turn the InterPro annotation file (match\_complete.xml.gz) found on
\url{https://www.ebi.ac.uk/interpro/download.html} into a RADS database. This option is
used to compute the precomputed InterPro databases.\\
-s, --seqs & - & Sequence files. Are used in combination with the domain arrangement files.
If none is given all sequence lengths are set to 0.\\
-o, --out & - & The output prefix used to produce two files in format prefix.db and prefix.da.
Be aware that we currently do no support adding data to an existing data base.\\
\hline
\end{tabular}
\end{table}
The domain arrangement file as well as the sequence files can contain several sequences/arrangements.
