Count the number of acidic, basic and neutral amino acids

Copy the below code and save it as " count-of-aminoacids.pl " on your system.

# This script will count the number of acidic/basic/neutral amino acids # While executing this script it asks for the file name of the protein sequence. If the sequence file is not available in the same directory of this script, enter the name of the file along with the path. eg.In windows: c:\proteinfile.txt, In Linux: /home/user/sequence/proteinfile.txt print "\n\n\t\#################### Count the number of acidic/basic/neutral amino acids #################### \n\n"; print "This script will count the number of acidic/basic/neutral amino acids\n\n"; use strict; #variables my $count_of_acidic=0; my $count_of_basic=0; my $count_of_neutral=0; my @prot; my $prot_filename; my $line; my $sequence; my $aa; print "PLEASE ENTER THE FILENAME OF THE PROTEIN SEQUENCE:="; chomp($prot_filename=<STDIN>); open(PROTFILE,$prot_filename) or die "unable to open the file"; @prot=<PROTFILE>; close PROTFILE; foreach $line (@prot) { # discard blank line if ($line =~ /^\s*$/) { next; # discard comment line } elsif($line =~ /^\s*#/) { next; # discard fasta header line } elsif($line =~ /^>/) { next; # keep line, add to sequence string } else { $sequence .= $line; } } # remove non-sequence data (in this case, whitespace) from $sequence string $sequence =~ s/\s//g; @prot=split("",$sequence); #splits string into an array print " \nThe original PROTEIN file is:\n$sequence \n"; while(@prot){ $aa = shift (@prot); if($aa =~/[DNEQ]/ig){ $count_of_acidic++; } if($aa=~/[KRH]/ig){ $count_of_basic++; } if($aa=~/[DNEQKRH]/ig){ $count_of_neutral++; } } print "\nNumber of acidic amino acids:".$count_of_acidic."\n"; print "Number of basic amino acids:".$count_of_basic."\n"; print "Number of neutral amino acids:".$count_of_neutral."\n";

Sample DNA Sequence - Save it as " proteinfile.txt "

NSFLIL__STVILS_RGYIGF_FCFQYDGCQCCPDS_YQVADFRSL_RIS ERNLLSS_CRLQVCPSTKSLPCGKWSCGGLF_FSKGSVYPRELQVPSPSST LKNAAGD_WAEQSDSTEDCRSHVRPADAAYAPKRSNVITWFFSYDSINSS_S SHGFQSLHTTSWDGPRSCRTCTKYTCSDSWKPTSCNARSCWPKTDAFR_TGGLP

Result for count-of-aminoacids.pl

>> perl count-of-aminoacids.pl #################### Count the number of acidic/basic/neutral amino acids #################### This script will count the number of acidic/basic/neutral amino acids PLEASE ENTER THE FILENAME OF THE PROTEIN SEQUENCE:=../bioseq/proteinfile.txt The original PROTEIN file is: NSFLIL__STVILS_RGYIGF_FCFQYDGCQCCPDS_YQVADFRSL_RISERNLLSS_CRLQVCPSTKSLPCGKWSCGGLF_FSKGSVYPRELQVPSPSSTLKNAAGD_WAEQSDSTEDCRSHVRPADAAYAPKRSNVITWFFSYDSINSS_SSHGFQSLHTTSWDGPRSCRTCTKYTCSDSWKPTSCNARSCWPKTDAFR_TGGLP