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Some grammar improvements.

Peter: Resolved conflicts during merge
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1 parent ca7762e commit 38e4c56a92ca83a0b642c96bf2206f5064cc8938 @cbrueffer cbrueffer committed with peterjc Dec 25, 2012
Showing with 9 additions and 7 deletions.
  1. +9 −7 Doc/Tutorial.tex
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16 Doc/Tutorial.tex
@@ -11377,10 +11377,10 @@ \section{Future plans}
\chapter{Sequence motif analysis using Bio.motifs}
This chapter gives an overview of the functionality of the
-\verb|Bio.motifs| package included in Biopython distribution. It is intended
-for people who are involved in analysis of sequence motif, so I'll
+\verb|Bio.motifs| package included in Biopython. It is intended
+for people who are involved in the analysis of sequence motifs, so I'll
assume that you are familiar with basic notions of motif analysis. In
-case something is unclear, please look into Section~\ref{sec:links}
+case something is unclear, please look at Section~\ref{sec:links}
for some relevant links.
Most of this chapter describes the new \verb|Bio.motifs| package included
@@ -11390,7 +11390,7 @@ \chapter{Sequence motif analysis using Bio.motifs}
most of their functionality with a unified motif object implementation.
Speaking of other libraries, if you are reading this you might be
-interested in the \href{http://fraenkel.mit.edu/TAMO/}{TAMO}, another Python library
+interested in \href{http://fraenkel.mit.edu/TAMO/}{TAMO}, another python library
designed to deal with sequence motifs. It supports more \emph{de-novo}
motif finders, but it is not a part of Biopython and has some restrictions
on commercial use.
@@ -11524,7 +11524,7 @@ \subsection{Creating a motif from instances}
>>> m.degenerate_consensus
Seq('WACVC', IUPACAmbiguousDNA())
\end{verbatim}
-Here, W and R follow the IUPAC nucleotide ambiguity codes: W is either A or T, and V is A, C, or G \cite{cornish1985}. The degenerate consensus sequence is constructed followed the rules specified by Cavener \cite{cavener1987}.
+Here, W and R follow the IUPAC nucleotide ambiguity codes: W is either A or T, and V is A, C, or G \cite{cornish1985}. The degenerate consensus sequence is constructed following the rules specified by Cavener \cite{cavener1987}.
We can also get the reverse complement of a motif:
%cont-doctest
@@ -11560,8 +11560,10 @@ \subsection{Reading motifs}
\subsubsection*{JASPAR}
One of the most popular motif databases \href{http://jaspar.genereg.net}{JASPAR}
- stores motifs either as a list of instances, or as a frequency matrix.
-As an example, these are the beginning and ending lines of the JASPAR \verb+Arnt.sites+ file showing known binding sites of the mouse helix-loop-helix transcription factor Arnt:
+stores motifs either as a list of instances, or as a frequency matrix.
+As an example, these are the beginning and ending lines of the JASPAR
+\verb+Arnt.sites+ file showing known binding sites of the mouse
+helix-loop-helix transcription factor Arnt:
\begin{verbatim}
>MA0004 ARNT 1
CACGTGatgtcctc

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