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\newlabel{lab_resources_pwmscan_pipeline}{{6.1}{78}{\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 matrices or count matrices are also accepted and are converted into PWMs. 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 regions corresponding to the sequences achieving a score at least as good as the threshold score are then returned under BED format. Figure and legend taken and adapted from \citep{ambrosini_pwmscan:_2018}.\relax}{figure.caption.33}{}}
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\@writefile{lof}{\contentsline{figure}{\numberline{6.2}{\ignorespaces\textbf{Benchmark :} PWMScan speed performances were measured and compared with 6 other well known genome scanners. In all cases, the h19 genome sequence was scanned with a 19bp CTCF matrix and a 11bp STAT1 matrix, 10 times. The run times are represented as boxplots. For PWMScan, both pwm\_scan and Bowtie strategies were run. Figure and legend taken and adapted from \citep{ambrosini_pwmscan:_2018}.\relax}}{79}{figure.caption.34}}
\newlabel{lab_resources_pwmscan_benchmark}{{6.2}{79}{\textbf{Benchmark :} PWMScan speed performances were measured and compared with 6 other well known genome scanners. In all cases, the h19 genome sequence was scanned with a 19bp CTCF matrix and a 11bp STAT1 matrix, 10 times. The run times are represented as boxplots. For PWMScan, both pwm\_scan and Bowtie strategies were run. Figure and legend taken and adapted from \citep{ambrosini_pwmscan:_2018}.\relax}{figure.caption.34}{}}
\@writefile{lot}{\contentsline{table}{\numberline{6.1}{\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. Table and legend taken and adapted from \citep{ambrosini_pwmscan:_2018}.\relax}}{80}{table.caption.35}}
\newlabel{lab_resources_pwmscan_benchmark_table}{{6.1}{80}{\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. Table and legend taken and adapted from \citep{ambrosini_pwmscan:_2018}.\relax}{table.caption.35}{}}