1\section{Profile construction steps, in detail}
2\label{section:pipeline}
3\setcounter{footnote}{0}
4
5\begin{description}
6
7\item [\textbf{Read and validate input alignment}]
8
9\item [\textbf{Calculate relative sequence weights}]
10
11\item [\textbf{Define sequence fragments}]
12
13\item [\textbf{Determine model architecture}]
14
15\item [\textbf{Calculate effective sequence number}]
16
17\item [\textbf{Parameterize the model}]
18
19\item [\textbf{Transfer annotation from MSA to model}]
20
21\item [\textbf{Calibrate the model}]
22
23\item [\textbf{Create the ``post'' MSA}]
24
25\end{description}
26
27In more detail, each step is described in the following
28subsections.\footnote{To study the relevant source code, start with
29  \ccode{p7\_builder.c::p7\_Builder()}.}
30
31
32\subsection{Alignment input and validation}
33
34HMMER is designed to work on input
35
36
37\subsection{Relative sequence weighting}
38
39\subsection{Sequence fragment definition}
40
41\subsection{Model architecture determination}
42
43\subsection{Effective sequence number (absolute sequence weights)}
44
45\subsection{Model parameterization}
46
47\subsection{Annotation transfer from MSA to model}
48
49\subsection{Model calibration}
50
51\subsection{Create the ``post'' MSA}
52
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