perl algorithm (ActiveState Software Inc)

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ActiveState Software Inc perl algorithm

DNA unwinding by AddA N B N is characterized by pauses and bursts of activity. ( A ) Example of how a single time-course can be segmented into pauses and unwinding phases. The raw intensity data (light blue open circle) were smoothed by running average using an optimum window size (shown as pink and dark blue lines). Then, the first derivative at every time point was calculated (grey open circle). If the derivative trace (grey open circle) is smoothed using an median filter (black line), then the histogram of the smoothed derivative values (inset) reveals two populations, one corresponding the pauses (clustered around zero) and one to the unwinding phases (clustered around 17 cpp). Thresholding ( Thr. ) of the derivative data (dashed line) allows the original intensity trace to be segmented into pauses (< Thr. , pink lines) and unwinding phases (> Thr. , dark lines). ( B–E ) To automatically analyze all data, a custom-written <t>PERL</t> algorithm was used (see ‘Materials and methods’ section). Using this algorithm, the distributions of the number of pauses per event (B), the duration of pauses (C), maximum rate of unwinding (D) and duration of unwinding phase (E) were obtained for 1 mM ATP (circle) and 3 μM ATP (triangle). All distributions are presented as percentage frequency, normalized to the maximum.

Perl Algorithm, supplied by ActiveState Software Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/custom-written+computer+program/perl+program/pmc02910053-69-10-13
Average 90 stars, based on 1 article reviews

perl algorithm - by Bioz Stars, 2026-10

90/100 stars

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Article Title: Visualizing helicases unwinding DNA at the single molecule level

Journal: Nucleic Acids Research

doi: 10.1093/nar/gkq173

Figure Legend Snippet: DNA unwinding by AddA N B N is characterized by pauses and bursts of activity. ( A ) Example of how a single time-course can be segmented into pauses and unwinding phases. The raw intensity data (light blue open circle) were smoothed by running average using an optimum window size (shown as pink and dark blue lines). Then, the first derivative at every time point was calculated (grey open circle). If the derivative trace (grey open circle) is smoothed using an median filter (black line), then the histogram of the smoothed derivative values (inset) reveals two populations, one corresponding the pauses (clustered around zero) and one to the unwinding phases (clustered around 17 cpp). Thresholding ( Thr. ) of the derivative data (dashed line) allows the original intensity trace to be segmented into pauses (< Thr. , pink lines) and unwinding phases (> Thr. , dark lines). ( B–E ) To automatically analyze all data, a custom-written PERL algorithm was used (see ‘Materials and methods’ section). Using this algorithm, the distributions of the number of pauses per event (B), the duration of pauses (C), maximum rate of unwinding (D) and duration of unwinding phase (E) were obtained for 1 mM ATP (circle) and 3 μM ATP (triangle). All distributions are presented as percentage frequency, normalized to the maximum.

Techniques Used: Activity Assay

other:

Article Title: ThermoPhyl: a software tool for selecting phylogenetically optimized conventional and quantitative-PCR taxon-targeted assays for use with complex samples.
Article Snippet: ThermoPhyl, a freeware PERL script program (download PERL from http://www.activestate.com/activeperl), is a simple matching program that runs on both windows and Unix machines.

Article Title: Visualizing helicases unwinding DNA at the single molecule level
Article Snippet: To identify and characterize the pauses and unwinding phases a custom-written PERL algorithm (ActiveState Software Inc.) was developed.

Gene Expression:

Article Title: A method for visualization of “omic” datasets for sphingolipid metabolism to predict potentially interesting differences
Article Snippet: .. Supplement 1A: Perl program to extract normalized glycosphingolipid gene expression values #!/usr/bin/Perl # microarray filtering file use strict; use warnings; my $Micro = $ARGV[0]; # Microarray file neme my $GeneList = $ARGV[1]; # Gene or probelist file open(MICRO, $Micro)||die"cannot open microarray file\n"; open(LIST, $GeneList)||die"cannot open genelist file\n"; my %hash= (); while(my $line = ){ chomp($line); my @words = split(/\t/,$line); my $id = $words[0]; $hash{$id} = 0; } my @keys = keys(%hash); my $num = @keys; while(my $gene = ) { chomp($gene); for(my $i=0; $i < $num; $i++) { my $key = $keys[$i]; chomp($key); if ($gene =~ m/$key/i) { print "$gene \n"; } } } close(MICRO); close(LIST); Instructions for using Perl program for filtering sphingolipid genes: on windows PC install the Activeperl package from www.activestate.com (Perl is already installed on Mac OS in the X‐terminal). ..

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perl algorithm (ActiveState Software Inc)

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