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ch_softwares.aux
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\citation{ambrosini_pwmscan:_2018}
\citation{khan_jaspar_2018}
\citation{kulakovskiy_hocomoco:_2018}
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\@writefile{lot}{\contentsline {table}{\numberline {1.1}{\ignorespaces \textbf {Motif scanning software comparison}. The performances of matrix\_scan were assessed by comparing how many of the regions listed by matrix\_scan were also returned by other programs and if the region scores were comparable. For the percentage of overlap with the match list returned by matrix\_scan, the shorter of the two lists always serves as the reference (100\%). For the score correlations with matrix\_scan scores, the Spearman correlation was used.\relax }}{5}{table.1.1}}
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\@writefile{lof}{\contentsline {figure}{\numberline {1.1}{\ignorespaces \textbf {PWMScan workflow :} the input is composed of a PWM and a score threshold specifying the minimum score for a sequence to achieved to be considered as a match. Letter probability matrix or count matrices are also accepted and are converted into PWM. The score threshold can also be given as a p-value or a percentage of the maximum score, in which case it is converted into a threshold score. Based on the length of the PWM, Bowtie or pwm\_scan can be used to find the matches on the genome. If Bowtie is used, the set of k-mers achieving a better score than the threshold score is computed using branch-and-bound algorithm (mba) and mapped on the genome. On the other hand, if matrix\_scan is used, the PWM is used to score every possible sub-sequence in the genome. The region achieving a score at least as good as the threshold score are then returned under BED format.\relax }}{6}{figure.caption.8}}
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\newlabel{softwares_pwmscan_pipeline}{{1.1}{6}{\textbf {PWMScan workflow :} the input is composed of a PWM and a score threshold specifying the minimum score for a sequence to achieved to be considered as a match. Letter probability matrix or count matrices are also accepted and are converted into PWM. The score threshold can also be given as a p-value or a percentage of the maximum score, in which case it is converted into a threshold score. Based on the length of the PWM, Bowtie or pwm\_scan can be used to find the matches on the genome. If Bowtie is used, the set of k-mers achieving a better score than the threshold score is computed using branch-and-bound algorithm (mba) and mapped on the genome. On the other hand, if matrix\_scan is used, the PWM is used to score every possible sub-sequence in the genome. The region achieving a score at least as good as the threshold score are then returned under BED format.\relax }{figure.caption.8}{}}
\citation{ambrosini_pwmscan:_2018}
\citation{langmead_ultrafast_2009}
\citation{bailey_meme_2009}
\citation{ambrosini_pwmscan:_2018}
\@writefile{lof}{\contentsline {figure}{\numberline {1.2}{\ignorespaces \textbf {Benchmark :} TODO.\relax }}{7}{figure.caption.9}}
\newlabel{softwares_pwmscan_benchmark}{{1.2}{7}{\textbf {Benchmark :} TODO.\relax }{figure.caption.9}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {1.1.2}Data and methods}{7}{subsection.1.1.2}}
\citation{ambrosini_pwmscan:_2018}
\citation{ambrosini_pwmscan:_2018}
\citation{ambrosini_chip-seq_2016}
\citation{ambrosini_pwmscan:_2018}
\@writefile{toc}{\contentsline {subsection}{\numberline {1.1.3}Benchmark}{9}{subsection.1.1.3}}
\@writefile{toc}{\contentsline {section}{\numberline {1.2}SPar-K}{9}{section.1.2}}
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