Perl script is designed to visualize virtually the features of nucleotide strings. …

• Preface
• I. Introduction
• II. Perl Notation
• III. Syntax
• 1. Perl program for calculating the arithmetic averages
• 2. Perl Program for calculating averages using subroutine
• 3. Perl program for concatenating two sequences
• 4. Perl program for file handling
• 5. Perl Program for File handling For Scalar And Array Variables
• 6. Perl program for calculating the length, total bases, GC and AT counts
• 7. Perl program depicting loop - functions
• 8. Perl program for DNA to RNA transcription
• 9. Perl program to operate array of variables
• 10. If and else operations
• 11. Retrieving protein sequences and locating motifs
• 12. In silico Salient features of DNA
• 13. Perl Program to translate DNA into protein
• 14. Bio-perl programme to retrieve DNA sequence from swissprot
• Appendix

This program uses the bioperl package to connect to the internet and get a Swissprot sequence from the internet databases using the get_sequence and is saved in $seq_object. The blast_sequence blasts a sequence against standard databases at NCBI and the result of the blast is stored in $blast_result. The write_blast writes a blast report out to a file. In this case the file name is raol1.blast.

1. #!/usr/bin/perl -w

1. use Bio::Perl;

1. $seq_object = get_sequence('swissprot', "ROA1_HUMAN");
2. $blast_result = blast_sequence($seq_object);
3. write_blast(">raol1.blast",$blast_result);
4. exit;