\@writefile{lof}{\contentsline {figure}{\numberline {6.1}{\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 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 }}{74}{figure.caption.33}}
\newlabel{lab_resources_pwmscan_pipeline}{{6.1}{74}{\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}{}}
\citation{ambrosini_chip-seq_2016}
\citation{ambrosini_signal_2003}
\citation{ambrosini_pwmscan:_2018}
\citation{ambrosini_pwmscan:_2018}
\citation{ambrosini_pwmscan:_2018}
\citation{ambrosini_pwmscan:_2018}
\citation{hertz_identification_1990}
\citation{beckstette_fast_2006}
\citation{turatsinze_using_2008}
\citation{heinz_simple_2010}
\citation{grant_fimo:_2011}
\citation{schones_statistical_2007}
\@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 }}{75}{figure.caption.34}}
\newlabel{lab_resources_pwmscan_benchmark}{{6.2}{75}{\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 }}{76}{table.caption.35}}
\newlabel{lab_resources_pwmscan_benchmark_table}{{6.1}{76}{\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}{}}