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\section{Profile construction steps, in detail}
\label{section:pipeline}
\setcounter{footnote}{0}
\begin{description}
\item [\textbf{Read and validate input alignment}]
\item [\textbf{Calculate relative sequence weights}]
\item [\textbf{Define sequence fragments}]
\item [\textbf{Determine model architecture}]
\item [\textbf{Calculate effective sequence number}]
\item [\textbf{Parameterize the model}]
\item [\textbf{Transfer annotation from MSA to model}]
\item [\textbf{Calibrate the model}]
\item [\textbf{Create the ``post'' MSA}]
\end{description}
In more detail, each step is described in the following
subsections.\footnote{To study the relevant source code, start with
\ccode{p7\_builder.c::p7\_Builder()}.}
\subsection{Alignment input and validation}
HMMER is designed to work on input
\subsection{Relative sequence weighting}
\subsection{Sequence fragment definition}
\subsection{Model architecture determination}
\subsection{Effective sequence number (absolute sequence weights)}
\subsection{Model parameterization}
\subsection{Annotation transfer from MSA to model}
\subsection{Model calibration}
\subsection{Create the ``post'' MSA}
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