Introduction to Bioinformatics

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Tony
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Introduction to Bioinformatics

Post by Tony » Thu Oct 01, 2009 1:06 am

Bioinformatics is the use of computers, software tools, and databases to handle biological information. Bioinformatics is widely used for genomics and proteomics. Bioinformatics helps to sequence and analyse all of the genomic entities, including genes and transcripts, in an organism. It also helps in proteonomics to analyse the complete set of proteins or proteome. Bioinformatics is used in drug designing and drug development. Bioinformatics is one of the fastest growing filed, which will certainly reveal the mysteries of life and many deceases. Bioinformatics has become a very important part of Biotechnology. All the information process by Biotechnology is stored and analysed using bioinformatics. Bioinformatics is the comprehensive application of mathematics, statistics, biochemistry, biophysics and computer algorithms to analyse biological data.

Application of Bioinformatics in various fields:
  • Drug designing
  • Drug development
  • Gene therapy
  • Evolutionary studies
  • Biotechnology
  • Bio-weapon creation
  • Veterinary medicine
  • Molecular medicine
  • Improve quality for various products
  • Climate change Studies
  • Waste recycling
  • Prevention medicine
  • Agriculture
  • Forensic analysis
  • Development of high yield crops
  • Antibiotic medicine
  • Pesticides
  • And More....
Skills Required for a Bioinformatician
As we know Bioinformatics is wide area, it will not be possible to learn all of them. The important topics that should be know are:

Molecular Biology
Should have a basic knowledge of molecular biology.

Experience with one or more of Molecular Biology software packages. Learn to use sequence analysis and molecular modelling software. Some of the molecular biology packages are BLAST, FASTA etc.

Computer's

Operating system's

Windows and Linux
Should have the basic knowledge of both windows and Linux. Nowadays Linux (Free open source) is widely used in bioinformatics for is robustness and available tools & software for this platform, its very important to learn these operating system.

Computer Programming Language
C/C++, Perl, Python, Java and HTML should be known by Bioinformatician.

Database Management Systems
Oracle and MySQL (Free Database Server) is widely used to store large biological data.

Sequence Analysis

Sequence analysis is the use of various bioinformatics methods and tools to determine the biological function and/or structure of genes and the proteins they code for.

How to perform Sequence Analysis?

To perform Sequence Similarity Search we use NCBI BLAST.

What is NCBI BLAST?
NCBI's BLAST, is used to compare the sequence of a particular gene or protein with other sequences from a variety of organisms.

What is BLAST?
BLAST (Basic Local Alignment Search Tool) is a set of programs designed to perform similarity searches on all available sequence data. We can use this searches to gain insight into the function and biological importance of gene products.

BLAST uses an algorithm developed by NCBI that seeks local alignment (the alignment of some portion of two sequences) as opposed to global alignment (the alignment of two sequences over their entire length). By searching for local alignments, BLAST is able to identify regions of similarity within two sequences.

Services provided by BLAST :

blastp - comparing an amino acid query sequence with others stored in protein sequence databases
blastn - comparing a nucleotide query sequence against a nucleotide sequence database
blastx - comparing a nucleotide query sequence translated in all reading frames with other amino acid sequences stored in protein sequence databases

To proceed with the BLAST we need the FASTA formatted Amino acid sequence.

How to obtain a FASTA Formatted Sequence?

Go to NCBI Home page.
Enter the Search option (eg: protein, Genome, etc) for any particular organism (eg: human, rat etc) and in the display option select FASTA.
Then click Go.
The FASTA sequence starts with > symbol.
eg: >gi|73535847|pdb|1Z9O|C Chain C, 1.9 Angstrom Crystal Structure Of The Rat Vap-A Msp Homology Domain In Complex With The Rat Orp1 Ffat Motif
GSHMAKHEQILVLDPPSDLKFKGPFTDVVTTNLKLQNPSDRKVCFKVKTTAPRRYCVRPNSGVIDPGSIV
TVSVMLQPFDYDPNEKSKHKFMVQTIFAPPNISDMEAVWKEAKPDELMDSKLRCVFEM

Copy the sequence.
From the home page click BLAST. Then you need to select the BLAST service you need to use like blastp, blastn etc.
Paste the sequence in the form.
Click on the BLAST button.

Analyse the result.

Bioinformatics Sequence Analysis Tools

Below listed are few online Sequence Analysis tools. We regularly add new websites and new tools in Bioinformatics. If you come across new tools in bioinformatics, please let us know.

Protein Sequence Analysis Tools
  • 3DCrunch - Database Browser of modelled Swiss-Prot proteins at ExPASy, Switzerland
  • 3D-Jigsaw - Comparative modelling server
  • AAT - Analysis and Annotation Tool for finding genes in genomic sequences
  • ASC - Analytic Surface Calculation of PDB molecules @t EMBL, Heidelberg)
  • BLOCKS Search - Search a protein against BLOCKS database
  • BTPRED - Prediction of beta-turns
  • CD-Search - Search a protein against CDD domain database
  • Chime - Plugin for structure view
  • Cn3D - Plugin for structure view for structure @ NCBI
  • eMOTIF Search - Assign putative function to new proteins by sequence comparison with IDENTIFY motif database.
  • Coils - Prediction of coiled Coil regions by Lupas method
  • CPHmodels - Structure prediction by comparative homology modelling
  • DIP - Search Database of Interacting Proteins
  • DOMPLOT - Structural domain organization annotated by ligand contacts.
  • eMATRIX Search - Predict function by sequence analysis using minimal-risk scoring matrices.
  • eMOTIF Maker - Generate motifs describing protein families or superfamilies
  • FingerPRINTScan - Search a protein sequence against protein motif fingerprints database
  • HMMTOP - Prediction of transmembrane helices and topology of proteins
  • JPred - Protein secondary structure prediction
  • LIBRA - LIght Balance for Remote Analogous proteins: search compatible structure of a target sequence by threading
  • Comparative modelling tools
  • Modules - Mobile protein domains database
  • MolSurfer - Calculate and navigate protein-protein interfaces
  • NetOGlyc - Prediction of O-glycosylation sites in mammalian proteins
  • nnPredict - Protein secondary structure prediction.
  • PFSCAN - Protein search against different profile databases
  • PPSearch - Search a protein sequence against prosite pattern database
  • Predicting Protein 3D structure based on homologous sequence search
  • RasMol - 3D viewer
  • VAST - Structure-structure similarity search
  • WebMol - 3D viewer

DNA / RNA Sequence Analysis Tools
  • Gene Finder -Exon and Splice Site Prediction
  • GENEID -Prediction of Exons and Gene Structure
  • ORD ID - Open Reading Frame search
  • ORF Finder - Open Reading Frame Finder
  • PatScan - DNA Sequence Motif search
Bioinformatics Databases

Below listed are few online Bioinformatics Databases. We regularly search and add new databases in Bioinformatics. If you come accross new database websites in bioinformatics, please let us know.

List of Bioinformatics Databases / Data Banks Online
  • NCBI - National Centre for Biotechnology Information (GenBank)
  • EBI - European Bioinformatics Institute (EMBL)
  • EMNEW - Index of New EMBL Nucleotides ( EBI)
  • DDBJ - DNA Data Bank of Japan
List of Protein Sequence Data Banks
  • SWISS-PROT - Protein sequence database
  • PIR - Protein Information Resource
  • MIPS - Munich Information centre for Protein Sequences
SeqAnalyser - Open Source BioPerl Software

What is SeqAnalyser?
SeqAnalyser is an open source bio perl software. It is used to Analyse both DNA and PROTIEN sequence.

Functions of SeqAnalyser?
  • PROTEIN Sequence Analysis
  • DNA Sequence Analysis
  • FORMAT Conversion
  • Convert DNA to PROTEIN
  • PAIRWISE Alignment
Sub Functions

PROTEIN Sequence Analysis
Getting Protien Structure
Search for Mottifs

DNA Sequence Analysis
Convert DNA to RNA
Convert RNA to DNA
Mutation of DNA
Frequency of NUCLIOTIDE
Reverse the DNA
Search for Mottifs
Reverse Compliment of DNA

FORMAT Conversion
Convert RAW Format Sequence
Convert FASTA Format Sequence
Convert GENBANK Format Sequence
Convert EMBL Format Sequence
Convert GCG Format Sequence

You can convert any of these format sequence file from one format to another

SeqAnalyser Download Procedure

Before you download our Software "SeqAnalyser" you need to download and install Perl and Bioperl.

Perl - Download Perl

After Downloading Install perl to your C:\ Drive

BioPerl - Download BioPerl

You get the zip file of BioPerl. Unzip it, Copy the contents inside the main folder and paste it in your perl\lib directory.

Contact us to get your login details to Download SeqAnalyser. Please make sure you have received Login details to download SeqAnalyser.

Download SeqAnalyser

If you have any issue Downloading SeqAnalyser, Please contact us.


Bioinformatics Perl Script Library
Perl is the most widely used programming language in Bioinformatics. You can download and use any scripts from our Bioinformatics Perl scripts library for FREE. If you are interested in programming and willing to share your bioinformatics scripts, you are welcome to share it with us. We will list your script in our script library and provide it for FREE.


dna2rna.pl
This Perl script "dna2rna.pl" can be used to convert the DNA sequence to RNA sequence. While running this Perl script it asks for the DNA file sequence. Enter the filename of the DNA sequence and it generates the RNA sequence. This script runs both on Windows and Linux operating Systems.

Code: Select all

# This script will convert your DNA sequence to RNA Sequence

# While executing this script it asks for the file name of the DNA 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:\dnafile.txt, In Linux: /home/user/sequence/dnafile.txt

print "\n\n\t\#################### DNA 2 RNA #################### \n\n";
print "This script will convert your DNA sequence to RNA Sequence\n\n";
print "ENTER THE FILENAME OF THE DNA SEQUENCE:= ";
$dnafilename = <STDIN>;
chomp $dnafilename;
unless ( open(DNAFILE, $dnafilename) ) {
    print "Cannot open file \"$dnafilename\"\n\n";
    goto h;
}
@DNA = <DNAFILE>;
close DNAFILE;
$DNA = join( '', @DNA);
print "The original DNA Sequence :=\n\n";
$DNA =~ s/\s//g;
print "$DNA\n\n";
$RNA = $DNA;
$RNA =~ s/T/U/g;
$RNA =~ s/t/u/g;
print "Transcribing DNA TO RNA :=\n\n";
print "$RNA\n";
<STDIN>;
Sample DNA Sequence - Save it as " dnafile.txt "

Code: Select all

AATTCATTTTTAATCCTTTAATAGTCCACAGTAATATTGTCCTAAAGAGGGTACATTGG
ATTTTAATTTTGCTTTCAATATGACGGCTGTCAATGTTGCCCTGATTCGTGATACCAAGTG
GCTGACTTTAGAAGTCTGTAGAGAATTTCAGAGAGGAACTTGCTCTCGAGCTGATGCAGATT
GCAAGTTTGCCCATCCACCAAGAGTTTGCCATGTGGAAAATGGTCGTGTGGTGGCCTGTTTTG
ATTCTCTAAAGGGTCGGTGTACCCGAGAGAACTGCAAGTACCTTCACCCTCCTCCACACTTAA
AAACGCAGCTGGAGATTAATGGGCGGAACAATCTGATTCAACAGAAGACTGCCGCAGCCATGTT
CGCCCAGCAGATGCAGCTTATGCTCCAAAACGCTCAAATGTCATCACTTGGTTCTTTTCCTATG
ACTCCATCAATTCCAGCTAATCCTCCCATGGCTTTCAATCCTTACATACCACATCCTGGGATGGG
CCTCGTTCCTGCAGAACTTGTACCAAATACACCTGTTCTGATTCCTGGAAACCCACCTCTTGCAAT
GCCAGGAGCTGTTGGCCCAAAACTGATGCGTTCAGATAAACTGGAGGTTTGCCGA
Result for dna2rna.pl

Code: Select all

 >> perl dna2rna.pl


        #################### DNA 2 RNA ####################

This script will convert your DNA sequence to RNA Sequence

ENTER THE FILENAME OF THE DNA SEQUENCE:= ../bioseq/dnafile.txt
The original DNA Sequence :=

AATTCATTTTTAATCCTTTAATAGTCCACAGTAATATTGTCCTAAAGAGGGTACATTGGATTTTAATTTTGCTTTCAATATGACGGCTGTCAATGTTGCCCTGATTCGTGATACCAAGTGGCTGACTTTAGAAGTCTGTAGAGAATTTCAGAGAGGAACTTGCTCTCGAGCTGATGCAGATTGCAAGTTTGCCCATCCACCAAGAGTTTGCCATGTGGAAAATGGTCGTGTGGTGGCCTGTTTTGATTCTCTAAAGGGTCGGTGTACCCGAGAGAACTGCAAGTACCTTCACCCTCCTCCACACTTAAAAACGCAGCTGGAGATTAATGGGCGGAACAATCTGATTCAACAGAAGACTGCCGCAGCCATGTTCGCCCAGCAGATGCAGCTTATGCTCCAAAACGCTCAAATGTCATCACTTGGTTCTTTTCCTATGACTCCATCAATTCCAGCTAATCCTCCCATGGCTTTCAATCCTTACATACCACATCCTGGGATGGGCCTCGTTCCTGCAGAACTTGTACCAAATACACCTGTTCTGATTCCTGGAAACCCACCTCTTGCAATGCCAGGAGCTGTTGGCCCAAAACTGATGCGTTCAGATAAACTGGAGGTTTGCCGA

Transcribing DNA TO RNA :=

AAUUCAUUUUUAAUCCUUUAAUAGUCCACAGUAAUAUUGUCCUAAAGAGGGUACAUUGGAUUUUAAUUUUGCUUUCAAUAUGACGGCUGUCAAUGUUGCCCUGAUUCGUGAUACCAAGUGGCUGACUUUAGAAGUCUGUAGAGAAUUUCAGAGAGGAACUUGCUCUCGAGCUGAUGCAGAUUGCAAGUUUGCCCAUCCACCAAGAGUUUGCCAUGUGGAAAAUGGUCGUGUGGUGGCCUGUUUUGAUUCUCUAAAGGGUCGGUGUACCCGAGAGAACUGCAAGUACCUUCACCCUCCUCCACACUUAAAAACGCAGCUGGAGAUUAAUGGGCGGAACAAUCUGAUUCAACAGAAGACUGCCGCAGCCAUGUUCGCCCAGCAGAUGCAGCUUAUGCUCCAAAACGCUCAAAUGUCAUCACUUGGUUCUUUUCCUAUGACUCCAUCAAUUCCAGCUAAUCCUCCCAUGGCUUUCAAUCCUUACAUACCACAUCCUGGGAUGGGCCUCGUUCCUGCAGAACUUGUACCAAAUACACCUGUUCUGAUUCCUGGAAACCCACCUCUUGCAAUGCCAGGAGCUGUUGGCCCAAAACUGAUGCGUUCAGAUAAACUGGAGGUUUGCCGA
rna2dna.pl
This Perl script "rna2dna.pl" can be used to convert the RNA sequence to DNA sequence. While running this Perl script it asks for the RNA file sequence. Enter the filename of the RNA sequence and it generates the DNA sequence. This script runs both on Windows and Linux operating Systems.

Code: Select all

# This script will convert your RNA sequence to DNA Sequence

# While executing this script it asks for the file name of the RNA 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:\rnafile.txt, In Linux: /home/user/sequence/rnafile.txt

print "\n\n\t\#################### RNA 2 DNA #################### \n\n";
print "This script will convert your RNA sequence to DNA Sequence\n\n";
print "ENTER THE FILENAME OF THE RNA SEQUENCE:= ";
$rnafilename = <STDIN>;
chomp $rnafilename;
unless ( open(RNAFILE, $rnafilename) ) {
    print "Cannot open file \"$rnafilename\"\n\n";
    goto h;
}
@RNA = <RNAFILE>;
close RNAFILE;
$RNA = join( '', @RNA);
print "The original RNA SEQUENCE :=\n\n";
$RNA =~ s/\s//g;
print "$RNA\n\n";
$DNA = $RNA;
$DNA =~ s/U/T/g;
$DNA =~ s/u/t/g;
print "TRANSCRIBING RNA TO DNA :=\n\n";
print "$DNA\n";
<STDIN>;
Sample DNA Sequence - Save it as " rnafile.txt "

Code: Select all

AAUUCAUUUUUAAUCCUUUAAUAGUCCACAGUAAUAUUGUCCUAAAGAGGGUACAUUGGAU
UUUAAUUUUGCUUUCAAUAUGACGGCUGUCAAUGUUGCCCUGAUUCGUGAUACCAAGUGGCU
GACUUUAGAAGUCUGUAGAGAAUUUCAGAGAGGAACUUGCUCUCGAGCUGAUGCAGAUUGCAA
GUUUGCCCAUCCACCAAGAGUUUGCCAUGUGGAAAAUGGUCGUGUGGUGGCCUGUUUUGAUUC
UCUAAAGGGUCGGUGUACCCGAGAGAACUGCAAGUACCUUCACCCUCCUCCACACUUAAAAAC
GCAGCUGGAGAUUAAUGGGCGGAACAAUCUGAUUCAACAGAAGACUGCCGCAGCCAUGUUCGC
CCAGCAGAUGCAGCUUAUGCUCCAAAACGCUCAAAUGUCAUCACUUGGUUCUUUUCCUAUGAC
UCCAUCAAUUCCAGCUAAUCCUCCCAUGGCUUUCAAUCCUUACAUACCACAUCCUGGGAUGGG
CCUCGUUCCUGCAGAACUUGUACCAAAUACACCUGUUCUGAUUCCUGGAAACCCACCUCUUGC
AAUGCCAGGAGCUGUUGGCCCAAAACUGAUGCGUUCAGAUAAACUGGAGGUUUGCCGA
Result for rna2dna.pl

Code: Select all

 >> perl rna2dna.pl


        #################### RNA 2 DNA ####################

This script will convert your RNA sequence to DNA Sequence

ENTER THE FILENAME OF THE RNA SEQUENCE:= ../bioseq/rnafile.txt
The original RNA SEQUENCE :=

AAUUCAUUUUUAAUCCUUUAAUAGUCCACAGUAAUAUUGUCCUAAAGAGGGUACAUUGGAUUUUAAUUUUGCUUUCAAUAUGACGGCUGUCAAUGUUGCCCUGAUUCGUGAUACCAAGUGGCUGACUUUAGAAGUCUGUAGAGAAUUUCAGAGAGGAACUUGCUCUCGAGCUGAUGCAGAUUGCAAGUUUGCCCAUCCACCAAGAGUUUGCCAUGUGGAAAAUGGUCGUGUGGUGGCCUGUUUUGAUUCUCUAAAGGGUCGGUGUACCCGAGAGAACUGCAAGUACCUUCACCCUCCUCCACACUUAAAAACGCAGCUGGAGAUUAAUGGGCGGAACAAUCUGAUUCAACAGAAGACUGCCGCAGCCAUGUUCGCCCAGCAGAUGCAGCUUAUGCUCCAAAACGCUCAAAUGUCAUCACUUGGUUCUUUUCCUAUGACUCCAUCAAUUCCAGCUAAUCCUCCCAUGGCUUUCAAUCCUUACAUACCACAUCCUGGGAUGGGCCUCGUUCCUGCAGAACUUGUACCAAAUACACCUGUUCUGAUUCCUGGAAACCCACCUCUUGCAAUGCCAGGAGCUGUUGGCCCAAAACUGAUGCGUUCAGAUAAACUGGAGGUUUGCCGA

TRANSCRIBING RNA TO DNA :=

AATTCATTTTTAATCCTTTAATAGTCCACAGTAATATTGTCCTAAAGAGGGTACATTGGATTTTAATTTTGCTTTCAATATGACGGCTGTCAATGTTGCCCTGATTCGTGATACCAAGTGGCTGACTTTAGAAGTCTGTAGAGAATTTCAGAGAGGAACTTGCTCTCGAGCTGATGCAGATTGCAAGTTTGCCCATCCACCAAGAGTTTGCCATGTGGAAAATGGTCGTGTGGTGGCCTGTTTTGATTCTCTAAAGGGTCGGTGTACCCGAGAGAACTGCAAGTACCTTCACCCTCCTCCACACTTAAAAACGCAGCTGGAGATTAATGGGCGGAACAATCTGATTCAACAGAAGACTGCCGCAGCCATGTTCGCCCAGCAGATGCAGCTTATGCTCCAAAACGCTCAAATGTCATCACTTGGTTCTTTTCCTATGACTCCATCAATTCCAGCTAATCCTCCCATGGCTTTCAATCCTTACATACCACATCCTGGGATGGGCCTCGTTCCTGCAGAACTTGTACCAAATACACCTGTTCTGATTCCTGGAAACCCACCTCTTGCAATGCCAGGAGCTGTTGGCCCAAAACTGATGCGTTCAGATAAACTGGAGGTTTGCCGA
dna2protein.pl
This Perl script "dna2protein.pl" can be used to convert the DNA sequence to Protein sequence. While running this Perl script it asks for the DNA file sequence. Enter the filename of the DNA sequence and it generates the Protein sequence. This script runs both on Windows and Linux operating Systems.

Code: Select all

# This script will convert your DNA sequence to PROTEIN Sequence

# While executing this script it asks for the file name of the DNA 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:\dnafile.txt, In Linux: /home/user/sequence/dnafile.txt

print "\n\n\t\#################### DNA 2 PROTEIN #################### \n\n";
print "This script will convert your DNA sequence to PROTEIN Sequence\n\n";
print "ENTER THE FILENAME OF THE DNA SEQUENCE:= ";
$DNAfilename = <STDIN>;
chomp $DNAfilename;
unless ( open(DNAFILE, $DNAfilename) ) {
    print "Cannot open file \"$DNAfilename\"\n\n";
}
@DNA = <DNAFILE>;
close DNAFILE;
$DNA = join( '', @DNA);
print " \nThe original DNA file is:\n$DNA \n";
$DNA =~ s/\s//g;
my $protein='';
my $codon;
for(my $i=0;$i<(length($DNA)-2);$i+=3)
{
$codon=substr($DNA,$i,3);
$protein.=&codon2aa($codon);
}
print "The translated protein is :\n$protein\n";
<STDIN>;

sub codon2aa{
my($codon)=@_;
$codon=uc $codon;
my(%g)=('TCA'=>'S','TCC'=>'S','TCG'=>'S','TCT'=>'S','TTC'=>'F','TTT'=>'F','TTA'=>'L','TTG'=>'L','TAC'=>'Y','TAT'=>'Y','TAA'=>'_','TAG'=>'_','TGC'=>'C','TGT'=>'C','TGA'=>'_','TGG'=>'W','CTA'=>'L','CTC'=>'L','CTG'=>'L','CTT'=>'L','CCA'=>'P','CCC'=>'P','CCG'=>'P','CCT'=>'P','CAC'=>'H','CAT'=>'H','CAA'=>'Q','CAG'=>'Q','CGA'=>'R','CGC'=>'R','CGG'=>'R','CGT'=>'R','ATA'=>'I','ATC'=>'I','ATT'=>'I','ATG'=>'M','ACA'=>'T','ACC'=>'T','ACG'=>'T','ACT'=>'T','AAC'=>'N','AAT'=>'N','AAA'=>'K','AAG'=>'K','AGC'=>'S','AGT'=>'S','AGA'=>'R','AGG'=>'R','GTA'=>'V','GTC'=>'V','GTG'=>'V','GTT'=>'V','GCA'=>'A','GCC'=>'A','GCG'=>'A','GCT'=>'A','GAC'=>'D','GAT'=>'D','GAA'=>'E','GAG'=>'E','GGA'=>'G','GGC'=>'G','GGG'=>'G','GGT'=>'G');
if(exists $g{$codon})
{
return $g{$codon};
}
else
{
print STDERR "Bad codon \"$codon\"!!\n";
exit;
}
}
Sample DNA Sequence - Save it as " dnafile.txt "

Code: Select all

AATTCATTTTTAATCCTTTAATAGTCCACAGTAATATTGTCCTAAAGAGGGTACATTGG
ATTTTAATTTTGCTTTCAATATGACGGCTGTCAATGTTGCCCTGATTCGTGATACCAAGTG
GCTGACTTTAGAAGTCTGTAGAGAATTTCAGAGAGGAACTTGCTCTCGAGCTGATGCAGATT
GCAAGTTTGCCCATCCACCAAGAGTTTGCCATGTGGAAAATGGTCGTGTGGTGGCCTGTTTTG
ATTCTCTAAAGGGTCGGTGTACCCGAGAGAACTGCAAGTACCTTCACCCTCCTCCACACTTAA
AAACGCAGCTGGAGATTAATGGGCGGAACAATCTGATTCAACAGAAGACTGCCGCAGCCATGTT
CGCCCAGCAGATGCAGCTTATGCTCCAAAACGCTCAAATGTCATCACTTGGTTCTTTTCCTATG
ACTCCATCAATTCCAGCTAATCCTCCCATGGCTTTCAATCCTTACATACCACATCCTGGGATGGG
CCTCGTTCCTGCAGAACTTGTACCAAATACACCTGTTCTGATTCCTGGAAACCCACCTCTTGCAAT
GCCAGGAGCTGTTGGCCCAAAACTGATGCGTTCAGATAAACTGGAGGTTTGCCGA
Result for dna2protein.pl

Code: Select all

 >> perl dna2protien.pl


        #################### DNA 2 PROTEIN ####################

This script will convert your DNA sequence to PROTEIN Sequence

ENTER THE FILENAME OF THE DNA SEQUENCE:= ../bioseq/dnafile.txt

The original DNA file is:
AATTCATTTTTAATCCTTTAATAGTCCACAGTAATATTGTCCTAAAGAGGGTACATTGG
ATTTTAATTTTGCTTTCAATATGACGGCTGTCAATGTTGCCCTGATTCGTGATACCAAGTG
GCTGACTTTAGAAGTCTGTAGAGAATTTCAGAGAGGAACTTGCTCTCGAGCTGATGCAGATT
GCAAGTTTGCCCATCCACCAAGAGTTTGCCATGTGGAAAATGGTCGTGTGGTGGCCTGTTTTG
ATTCTCTAAAGGGTCGGTGTACCCGAGAGAACTGCAAGTACCTTCACCCTCCTCCACACTTAA
AAACGCAGCTGGAGATTAATGGGCGGAACAATCTGATTCAACAGAAGACTGCCGCAGCCATGTT
CGCCCAGCAGATGCAGCTTATGCTCCAAAACGCTCAAATGTCATCACTTGGTTCTTTTCCTATG
ACTCCATCAATTCCAGCTAATCCTCCCATGGCTTTCAATCCTTACATACCACATCCTGGGATGGG
CCTCGTTCCTGCAGAACTTGTACCAAATACACCTGTTCTGATTCCTGGAAACCCACCTCTTGCAAT
GCCAGGAGCTGTTGGCCCAAAACTGATGCGTTCAGATAAACTGGAGGTTTGCCGA

The translated protein is :
NSFLIL__STVILS_RGYIGF_FCFQYDGCQCCPDS_YQVADFRSL_RISERNLLSS_CRLQVCPSTKSLPCGKWSCGGLF_FSKGSVYPRELQVPSPSSTLKNAAGD_WAEQSDSTEDCRSHVRPADAAYAPKRSNVITWFFSYDSINSS_SSHGFQSLHTTSWDGPRSCRTCTKYTCSDSWKPTSCNARSCWPKTDAFR_TGGLP
dnafrequency.pl
This script "dnafrequency.pl" can be used to calculate the frequency of nucleotides in the DNA sequence. While running this script it asks for the filename of the DNA sequence. Enter the filename of the DNA sequence and it calculates the frequency of the nucleotides in the DNA sequence.

Code: Select all

# This script will count the number of Adenine, Thymine, Guanine and Cytosine in your DNA Sequence

# While executing this script it asks for the file name of the DNA 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:\dnafile.txt, In Linux: /home/user/sequence/dnafile.txt


print "\n\n\t\#################### FREQUENCY OF NUCLIOTIDE #################### \n\n";
print "This script will count the number of Adenine, Thymine, Guanine and Cytosine in your DNA Sequence\n\n";
print "ENTER THE FILENAME OF THE DNA SEQUENCE:= ";
$dna_filename = <STDIN>;
chomp $dna_filename;
unless ( open(DNAFILE, $dna_filename) ) 
{
	print "Sorry the file does not exist!!! \n";
	print "Cannot open file \"$dna_filename\"\n";
	die;
}
@DNA = <DNAFILE>;
close DNAFILE;
$DNA = join( '', @DNA);
print " \n The original DNA file is:\n  $DNA \n";
$DNA =~ s/\s//g;
@DNA = split( '', $DNA );
$count_of_A = 0;
$count_of_C = 0;
$count_of_G = 0;
$count_of_T = 0;
$errors     = 0;
foreach $base (@DNA) {

    if     ( $base eq  'a' ) {
        ++$count_of_A;
    } elsif ( $base eq 'c' ) {
        ++$count_of_C;
    } elsif ( $base eq 'g' ) {
        ++$count_of_G;
    } elsif ( $base eq 't' ) {
        ++$count_of_T;
    }
        elsif ( $base eq 'T' ) {
        ++$count_of_T; }

        elsif ( $base eq 'C' ) {
        ++$count_of_C; }
        elsif ( $base eq 'A' ) {
        ++$count_of_A; }
        elsif ( $base eq 'G' ) {
        ++$count_of_G; }

        else {
        print "Error - Unknown base: $base\n";
        ++$errors;
    }
}
print "Adenine = $count_of_A\n";
print "Cytosine = $count_of_C\n";
print "Guanine = $count_of_G\n";
print "Thymine = $count_of_T\n";

if ($errors) {
        print "There were $errors unrecognized bases.\n";
}
Sample DNA Sequence - Save it as " dnafile.txt "

Code: Select all

AATTCATTTTTAATCCTTTAATAGTCCACAGTAATATTGTCCTAAAGAGGGTACATTGG
ATTTTAATTTTGCTTTCAATATGACGGCTGTCAATGTTGCCCTGATTCGTGATACCAAGTG
GCTGACTTTAGAAGTCTGTAGAGAATTTCAGAGAGGAACTTGCTCTCGAGCTGATGCAGATT
GCAAGTTTGCCCATCCACCAAGAGTTTGCCATGTGGAAAATGGTCGTGTGGTGGCCTGTTTTG
ATTCTCTAAAGGGTCGGTGTACCCGAGAGAACTGCAAGTACCTTCACCCTCCTCCACACTTAA
AAACGCAGCTGGAGATTAATGGGCGGAACAATCTGATTCAACAGAAGACTGCCGCAGCCATGTT
CGCCCAGCAGATGCAGCTTATGCTCCAAAACGCTCAAATGTCATCACTTGGTTCTTTTCCTATG
ACTCCATCAATTCCAGCTAATCCTCCCATGGCTTTCAATCCTTACATACCACATCCTGGGATGGG
CCTCGTTCCTGCAGAACTTGTACCAAATACACCTGTTCTGATTCCTGGAAACCCACCTCTTGCAAT
GCCAGGAGCTGTTGGCCCAAAACTGATGCGTTCAGATAAACTGGAGGTTTGCCGA
Result for dnafrequency.pl

Code: Select all

 >> perl dnafrequency.pl


        #################### FREQUENCY OF NUCLIOTIDE ####################

This script will count the number of Adenine, Thymine, Guanine and Cytosine in your DNA Sequence

ENTER THE FILENAME OF THE DNA SEQUENCE:= ../bioseq/dnafile.txt

 The original DNA file is:
  AATTCATTTTTAATCCTTTAATAGTCCACAGTAATATTGTCCTAAAGAGGGTACATTGG
ATTTTAATTTTGCTTTCAATATGACGGCTGTCAATGTTGCCCTGATTCGTGATACCAAGTG
GCTGACTTTAGAAGTCTGTAGAGAATTTCAGAGAGGAACTTGCTCTCGAGCTGATGCAGATT
GCAAGTTTGCCCATCCACCAAGAGTTTGCCATGTGGAAAATGGTCGTGTGGTGGCCTGTTTTG
ATTCTCTAAAGGGTCGGTGTACCCGAGAGAACTGCAAGTACCTTCACCCTCCTCCACACTTAA
AAACGCAGCTGGAGATTAATGGGCGGAACAATCTGATTCAACAGAAGACTGCCGCAGCCATGTT
CGCCCAGCAGATGCAGCTTATGCTCCAAAACGCTCAAATGTCATCACTTGGTTCTTTTCCTATG
ACTCCATCAATTCCAGCTAATCCTCCCATGGCTTTCAATCCTTACATACCACATCCTGGGATGGG
CCTCGTTCCTGCAGAACTTGTACCAAATACACCTGTTCTGATTCCTGGAAACCCACCTCTTGCAAT
GCCAGGAGCTGTTGGCCCAAAACTGATGCGTTCAGATAAACTGGAGGTTTGCCGA
count-of-aminoacids.pl
This script "count-of-aminoacids.pl" can be used to calculate the count of acidic , basic and neutral amino acids in a protein sequence. While running this script it asks for the filename of the Protein sequence. Enter the filename of the Protein sequence and it calculates the total count of acidic , basic and neutral amino acids in the Protein sequence.

Code: Select all

# 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 "

Code: Select all

NSFLIL__STVILS_RGYIGF_FCFQYDGCQCCPDS_YQVADFRSL_RIS
ERNLLSS_CRLQVCPSTKSLPCGKWSCGGLF_FSKGSVYPRELQVPSPSST
LKNAAGD_WAEQSDSTEDCRSHVRPADAAYAPKRSNVITWFFSYDSINSS_S
SHGFQSLHTTSWDGPRSCRTCTKYTCSDSWKPTSCNARSCWPKTDAFR_TGGLP
Result for count-of-aminoacids.pl

Code: Select all

 >> 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
motifs.pl
This script "motifs.pl" can be used to find the motifs in a DNA sequence. While running this script it asks for the filename of the DNA sequence and the motifs to search. It will search for the required motif in the sequence.

Code: Select all

# This script will find the motifs in a DNA sequence

# While executing this script it asks for the file name of the DNA 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:\dnafile.txt, In Linux: /home/user/sequence/dnafile.txt

print "\n\n\t\#################### motifs in  DNA SEQUENCE #################### \n\n";
print "This script find the motifs in a DNA sequence\n\n";
print "ENTER THE FILENAME OF THE DNA SEQUENCE:= ";
$dnafilename = <STDIN>;
chomp $dnafilename;
unless ( open(dnafilename, $dnafilename) ) {
	print "Cannot open file \"$dnafilename\"\n\n";
	exit;
}
@protein = <dnafilename>;
close dnafilename;
$protein = join( '', @protein);
$protein =~ s/\s//g;
do {
    print "ENTER A MOTIF {Sequence} TO SEARCH FOR := ";
    $motif = <STDIN>;
    chomp $motif;
    if ( $protein =~ /$motif/ ) {
        print "Found it!\n\n";
exit;
    } else {
        print "Not found.\n\n";
exit;
    }
} until ( $motif =~ /^\s*$/ );
Sample DNA Sequence - Save it as " dnafile.txt "

Code: Select all

AATTCATTTTTAATCCTTTAATAGTCCACAGTAATATTGTCCTAAAGAGGGTACATTGG
ATTTTAATTTTGCTTTCAATATGACGGCTGTCAATGTTGCCCTGATTCGTGATACCAAGTG
GCTGACTTTAGAAGTCTGTAGAGAATTTCAGAGAGGAACTTGCTCTCGAGCTGATGCAGATT
GCAAGTTTGCCCATCCACCAAGAGTTTGCCATGTGGAAAATGGTCGTGTGGTGGCCTGTTTTG
ATTCTCTAAAGGGTCGGTGTACCCGAGAGAACTGCAAGTACCTTCACCCTCCTCCACACTTAA
AAACGCAGCTGGAGATTAATGGGCGGAACAATCTGATTCAACAGAAGACTGCCGCAGCCATGTT
CGCCCAGCAGATGCAGCTTATGCTCCAAAACGCTCAAATGTCATCACTTGGTTCTTTTCCTATG
ACTCCATCAATTCCAGCTAATCCTCCCATGGCTTTCAATCCTTACATACCACATCCTGGGATGGG
CCTCGTTCCTGCAGAACTTGTACCAAATACACCTGTTCTGATTCCTGGAAACCCACCTCTTGCAAT
GCCAGGAGCTGTTGGCCCAAAACTGATGCGTTCAGATAAACTGGAGGTTTGCCGA
Result for motifs.pl

Code: Select all

perl motifs.pl


        #################### motifs in  DNA SEQUENCE####################

This script find the motifs in a DNA sequence

ENTER THE FILENAME OF THE DNA SEQUENCE:= ../bioseq/dnafile.txt
ENTER A MOTIF {Sequence} TO SEARCH FOR := azs
Not found.

==============================================================================

perl motifs.pl


        #################### motifs in  DNA SEQUENCE####################

This script find the motifs in a DNA sequence

ENTER THE FILENAME OF THE DNA SEQUENCE:= ../bioseq/dnafile.txt
ENTER A MOTIF {Sequence} TO SEARCH FOR := TCGGTGTACCCGAGAGAACTGCAAGTACCTTCA
Found it!
reverse-complement.pl
This script "reverse-complement.pl" can be used to find the reverse complement of a DNA Sequence. While running this script it asks for the filename of the DNA sequence. This script generates the reverse complement of a DNA Sequence. It will search for the required motif in the sequence.

Code: Select all

# This script can be used to find the Reverse Complement in a DNA Sequence.

# While executing this script it asks for the file name of the DNA sequence. 
# If the DNA sequence file is not in the same directory of this script, enter the file name with its full path.
# Example: 
# In windows:  c:\rnafile.txt 
# In Linux  : /home/user/sequence/rnafile.txt

# Send your comments and suggessions to techcuriosity @gmail.com
# Website : http://www.techcuriosity.com

use File::Path;
print "\n\t#################### GET REVERSE COMPLEMENT OF DNA ####################\n\n";
print "PLEASE TYPE THE FILENAME OF THE DNA SEQUENCE := ";
$dnafilename = <STDIN>;
chomp $dnafilename;
unless ( open(DNAFILE, $dnafilename) ) 
{
    print "Cannot open file \"$dnafilename\"\n\n";
    exit;
}
@DNA = <DNAFILE>;
close DNAFILE;
$DNA = join( '', @DNA);
$DNA =~ s/\s//g;
print "\nTHE ORIGINAL DNA SEQUENCE :=\n$DNA\n\n";
@DNA = split( '', $DNA );
print"REVERSE COMPLEMENT OF THE DNA SEQUENCE :=\n";

foreach $nucleotide(reverse(@DNA)) {



    if      ($nucleotide =~ /a/i) {
        print "T";
        print WRITE "T";
    } elsif ($nucleotide =~ /t/i) {
        print "A";
        print WRITE "A";
    } elsif ($nucleotide =~ /g/i) {
        print "C";
        print WRITE "C";
    } elsif ($nucleotide =~ /c/i) {
        print "G";
        print WRITE "G";
    } else {
        die "$0:  Bad nucleotide!  [$nucleotide]\n";
    }
}
Sample DNA Sequence - Save it as " dnafile.txt "

Code: Select all

AATTCATTTTTAATCCTTTAATAGTCCACAGTAATATTGTCCTAAAGAGGGTACATTGG
ATTTTAATTTTGCTTTCAATATGACGGCTGTCAATGTTGCCCTGATTCGTGATACCAAGTG
GCTGACTTTAGAAGTCTGTAGAGAATTTCAGAGAGGAACTTGCTCTCGAGCTGATGCAGATT
GCAAGTTTGCCCATCCACCAAGAGTTTGCCATGTGGAAAATGGTCGTGTGGTGGCCTGTTTTG
ATTCTCTAAAGGGTCGGTGTACCCGAGAGAACTGCAAGTACCTTCACCCTCCTCCACACTTAA
AAACGCAGCTGGAGATTAATGGGCGGAACAATCTGATTCAACAGAAGACTGCCGCAGCCATGTT
CGCCCAGCAGATGCAGCTTATGCTCCAAAACGCTCAAATGTCATCACTTGGTTCTTTTCCTATG
ACTCCATCAATTCCAGCTAATCCTCCCATGGCTTTCAATCCTTACATACCACATCCTGGGATGGG
CCTCGTTCCTGCAGAACTTGTACCAAATACACCTGTTCTGATTCCTGGAAACCCACCTCTTGCAAT
GCCAGGAGCTGTTGGCCCAAAACTGATGCGTTCAGATAAACTGGAGGTTTGCCGA
Result for reverse-complement.pl

Code: Select all

>> perl reverse-complement.pl

        #################### GET REVERSE COMPLEMENT OF DNA ####################

PLEASE TYPE THE FILENAME OF THE DNA SEQUENCE := ../bioseq/dnafile.txt

THE ORIGINAL DNA SEQUENCE :=
AATTCATTTTTAATCCTTTAATAGTCCACAGTAATATTGTCCTAAAGAGGGTACATTGGATTTTAATTTTGCTTTCAATATGACGGCTGTCAATGTTGCCCTGATTCGTGATACCAAGTGGCTGACTTTAGAAGTCTGTAGAGAATTTCAGAGAGGAACTTGCTCTCGAGCTGATGCAGATTGCAAGTTTGCCCATCCACCAAGAGTTTGCCATGTGGAAAATGGTCGTGTGGTGGCCTGTTTTGATTCTCTAAAGGGTCGGTGTACCCGAGAGAACTGCAAGTACCTTCACCCTCCTCCACACTTAAAAACGCAGCTGGAGATTAATGGGCGGAACAATCTGATTCAACAGAAGACTGCCGCAGCCATGTTCGCCCAGCAGATGCAGCTTATGCTCCAAAACGCTCAAATGTCATCACTTGGTTCTTTTCCTATGACTCCATCAATTCCAGCTAATCCTCCCATGGCTTTCAATCCTTACATACCACATCCTGGGATGGGCCTCGTTCCTGCAGAACTTGTACCAAATACACCTGTTCTGATTCCTGGAAACCCACCTCTTGCAATGCCAGGAGCTGTTGGCCCAAAACTGATGCGTTCAGATAAACTGGAGGTTTGCCGA

REVERSE COMPLEMENT OF THE DNA SEQUENCE :=
TCGGCAAACCTCCAGTTTATCTGAACGCATCAGTTTTGGGCCAACAGCTCCTGGCATTGCAAGAGGTGGGTTTCCAGGAATCAGAACAGGTGTATTTGGTACAAGTTCTGCAGGAACGAGGCCCATCCCAGGATGTGGTATGTAAGGATTGAAAGCCATGGGAGGATTAGCTGGAATTGATGGAGTCATAGGAAAAGAACCAAGTGATGACATTTGAGCGTTTTGGAGCATAAGCTGCATCTGCTGGGCGAACATGGCTGCGGCAGTCTTCTGTTGAATCAGATTGTTCCGCCCATTAATCTCCAGCTGCGTTTTTAAGTGTGGAGGAGGGTGAAGGTACTTGCAGTTCTCTCGGGTACACCGACCCTTTAGAGAATCAAAACAGGCCACCACACGACCATTTTCCACATGGCAAACTCTTGGTGGATGGGCAAACTTGCAATCTGCATCAGCTCGAGAGCAAGTTCCTCTCTGAAATTCTCTACAGACTTCTAAAGTCAGCCACTTGGTATCACGAATCAGGGCAACATTGACAGCCGTCATATTGAAAGCAAAATTAAAATCCAATGTACCCTCTTTAGGACAATATTACTGTGGACTATTAAAGGATTAAAAATGAA
mutation.pl
This script "mutation.pl" can be used to to mutate a DNA Sequence. While running this script it asks for the filename of the DNA sequence. This script randomly generates 10 successive mutation result.

Code: Select all

# This script can be used to Mutate a DNA Sequence.
# This script randomly mutates the DNA sequence and generates 10 successive mutation results.
# While executing this script it asks for the file name of the DNA sequence.
# If the DNA sequence file is not in the same directory of this script, enter the file name with its full path.
# Example:
# In windows:  c:\rnafile.txt
# In Linux  : /home/user/sequence/rnafile.txt

# Send your comments and suggestions to techcuriosity @gmail.com
# Website : http://www.techcuriosity.com

use File::Path;
print "\n\t#################### MUTATION OF DNA ####################\n\n";
print "ENTER THE FILENAME OF THE DNA SEQUENCE:= ";
$dnafilename = <STDIN>;
chomp $dnafilename;
unless ( open(DNAFILE, $dnafilename) ) 
{
    print "Cannot open file \"$dnafilename\"\n\n";
    goto h;
}
my $DNA = <DNAFILE>;
close DNAFILE;

my $i;
my $mutant;
$mutant = mutate($DNA);
print "Mutate DNA\n\n";
print "HERE IS THE ORIGINAL DNA SEQUENCE:\n";
print "$DNA\n\n";
print "HERE IS THE MUTANT DNA SEQUENCE:\n";
print "$mutant\n\n";
print "HERE ARE THE 10 SUCCESSIVE MUTATIONS:\n\n";
for ($i=0 ; $i < 10 ; ++$i)
  {
    $mutant = mutate($mutant);
    print "$mutant\n";
        print WRITE "$mutant\n";
  }

sub mutate
  {
        my($dna) = @_;
        my($position) = randomposition($dna);
        my $current_base = substr($dna, $position, 1);
        my $newbase;
    do
  {
        $newbase = randomnucleotide();
  }
        until ($newbase ne $current_base);
        substr($dna,$position,1,$newbase);
        return $dna;
  }
sub randomposition
  {
        my($string) = @_;
        return int rand length $string;
  }
sub randomelement
  {
    my(@array) = @_;
    return $array[rand @array];
  }
sub randomnucleotide
  {
    my(@nucleotides) = ('A', 'C', 'G', 'T');
    return randomelement(@nucleotides);
  }
Sample DNA Sequence - Save it as " dnafile.txt "

Code: Select all

AATTCATTTTTAATCCTTTAATAGTCCACAGTAATATTGTCCTAAAGAGGGTACATTGG
ATTTTAATTTTGCTTTCAATATGACGGCTGTCAATGTTGCCCTGATTCGTGATACCAAGTG
GCTGACTTTAGAAGTCTGTAGAGAATTTCAGAGAGGAACTTGCTCTCGAGCTGATGCAGATT
GCAAGTTTGCCCATCCACCAAGAGTTTGCCATGTGGAAAATGGTCGTGTGGTGGCCTGTTTTG
ATTCTCTAAAGGGTCGGTGTACCCGAGAGAACTGCAAGTACCTTCACCCTCCTCCACACTTAA
AAACGCAGCTGGAGATTAATGGGCGGAACAATCTGATTCAACAGAAGACTGCCGCAGCCATGTT
CGCCCAGCAGATGCAGCTTATGCTCCAAAACGCTCAAATGTCATCACTTGGTTCTTTTCCTATG
ACTCCATCAATTCCAGCTAATCCTCCCATGGCTTTCAATCCTTACATACCACATCCTGGGATGGG
CCTCGTTCCTGCAGAACTTGTACCAAATACACCTGTTCTGATTCCTGGAAACCCACCTCTTGCAAT
GCCAGGAGCTGTTGGCCCAAAACTGATGCGTTCAGATAAACTGGAGGTTTGCCGA
Result for mutation.pl

Code: Select all

>> perl mutation.pl

        #################### MUTATION OF DNA ####################

ENTER THE FILENAME OF THE DNA SEQUENCE:= ../bioseq/dnafile.txt
Mutate DNA

HERE IS THE ORIGINAL DNA SEQUENCE:
AATTCATTTTTAATCCTTTAATAGTCCACAGTAATATTGTCCTAAAGAGGGTACATTGGATTTTAATTTTGCTTTCAATATGACGGCTGTCAATGTTGCCCTGATTCGTGATACCAAGTG


HERE IS THE MUTANT DNA SEQUENCE:
AATTCATTCTTAATCCTTTAATAGTCCACAGTAATATTGTCCTAAAGAGGGTACATTGGATTTTAATTTTGCTTTCAATATGACGGCTGTCAATGTTGCCCTGATTCGTGATACCAAGTG


HERE ARE THE 10 SUCCESSIVE MUTATIONS:

AATTCATTCTTAATCCTTTAATAGTCCACAGTAATATTGTCCTAAAGAGGGTACATTGGATTTTAATTTTGCTTTCAATATGACGGCTGTCAATGTTGCCCTGATTCGGGATACCAAGTG

AATTCATTCTTAATCCTTTAATAGTCCACAGTAATATTGTCCTAAAGAGGGTACATTGGATTTTAATTTTGCTTTCAATATGACGGCTGTCAATGTTGCCCTGATTCGAGATACCAAGTG

AATTCTTTCTTAATCCTTTAATAGTCCACAGTAATATTGTCCTAAAGAGGGTACATTGGATTTTAATTTTGCTTTCAATATGACGGCTGTCAATGTTGCCCTGATTCGAGATACCAAGTG

AATTCTTTCTTAATCCTTTAATAGTCCACAGTAATATTGTCCTGAAGAGGGTACATTGGATTTTAATTTTGCTTTCAATATGACGGCTGTCAATGTTGCCCTGATTCGAGATACCAAGTG

AATTCTTTCTTAATCCTTTAATAGTCCACAGTAATATTGTCCTGAAGAGGGTACATTTGATTTTAATTTTGCTTTCAATATGACGGCTGTCAATGTTGCCCTGATTCGAGATACCAAGTG

AATTCTTTCTTAATCCTTTAATAGTCCACAGTAATATTGTCCTGAAGAGGGTACATTTGATTTTAATTTTGCTTTCAATATGACGGCTGTCAATGTTGCCCTGATTCGAGATACAAAGTG

AATTCTTTCTTAATCCTTTAATAGTCCACAGTAATATTGTCCTGAAGAGGGTACATTTGATTTTAATTTTGCTTTCAATATGACGGCTGTCAATGTTGCCCAGATTCGAGATACAAAGTG

AATTCTTTCTTAATCCTTTAATAGTACACAGTAATATTGTCCTGAAGAGGGTACATTTGATTTTAATTTTGCTTTCAATATGACGGCTGTCAATGTTGCCCAGATTCGAGATACAAAGTG

AATTCTTTCTTAATCCTTTAATAGTACCCAGTAATATTGTCCTGAAGAGGGTACATTTGATTTTAATTTTGCTTTCAATATGACGGCTGTCAATGTTGCCCAGATTCGAGATACAAAGTG

AATTCTTTCTTAATCCTTTAATAGTACCCAGTAATAATGTCCTGAAGAGGGTACATTTGATTTTAATTTTGCTTTCAATATGACGGCTGTCAATGTTGCCCAGATTCGAGATACAAAGTG
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