PERL , Perl is a family of high-level, general-purpose, interpreted, dynamic programming languages. The languages in this family include Perl 5 and Perl 6. Though Perl is not officially an acronym, there are various backronyms in use, such as: Practical Extraction and Reporting Language.[6] Perl was originally developed by Larry Wall in 1987 as a general-purpose Unix scripting language to make report processing easier.

1. 13.1
Pearl and Biopearl
Pearl and Biopearl
TOOLS FOR BIOINFORMATICS
TOOLS FOR BIOINFORMATICS
SUBMITTED BY :AAMIR
JAVED
MSc 1ST SEM
REG NO :11CQST2001
SUBMITTED TO : DR
T.S.MURALIDHAR
HOD OF
BIOTECHNOLOGY

2. ‫סקר הוראה‬
‫בשבועות הקרובים‬
‫יתקיים סקר‬
‫ההוראה‬
‫)‬
‫מידע אישי לתלמיד‬
‫(‬
‫2.31‬

3. 13.3
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CONTENTS
IntroductIon
BIo pearl modules
What Is perl ?
Why use perl ?
What’s BIoperl ?
Why BIoperl for B IoInformatIcs
thIngs We can do WIth BIoperl
conclusIon
aBstract
synopsIs
reference

4. 13.5
Introduction
Perl stands for Practical Extraction •
and Report Language •
(Author: Larry Wall (1986 •

5. 13.6
: Objective of BioPerl
 Develop
reusable, extensible core Perl modules
for use as a standard for manipulating
molecular biological data.
 Background:
 Started in 1995
 One of the oldest open source Bioinformatics
Toolkit Project
 http://bugzilla.BioPerl.org/

6. 13.7
?What is Perl
Perl is an interpreted programming language that •
resembles both a real programming language and
.a shell
A Language for easily manipulating text, files, and –
processes
Provides more concise and readable way to do jobs –
.formerly accomplished using C or shells
BioPerl-bugs@BioPerl.org
•

7. 13.8
?Why use Perl
Easy to use
Fast
Portability
Efficiency
Free to use
Correctness

8. 13.9
What’s BioPerl
The BioPerl project is an international association of developers of
open source Perl tools for bioinformatics, genomics and life science
research.
Things you can do with BioPerl:
• Read and write sequence files of different format, including: Fasta,
GenBank, EMBL, SwissProt and more…
• Extract gene annotation from GenBank, EMBL, SwissProt files
• Read and analyse BLAST results.
•Read and convert codons into amino acid and proteins.
• Read multiple sequence alignments.
• Analysing SNP data.

9. 13.10
Why Bioperl for Bio-informatics?
Perl is good at file manipulation and text
processing, which make up a large part of
. the routine tasks in bio-informatics
Perl language, documentation and many
.Perl packages are freely available
Perl is easy to get started in, to write small
. and medium-sized programs
BioPerl modules are called Bio::XXX
You can use the BioPerl wiki:
http:/bioperl.org

10. 13.11
Object-oriented use of packages
Many packages are meant to be used as objects.
In Perl, an object is a data structure that can use subroutines that are
associated with it.
obj$
0x225d14
func()
anotherFunc()
We will not learn object oriented programming,
but we will learn how to create and use objects defined by BioPerl packages.

11. 13.12
BLAST
Congrats, you just sequenced
.yourself some DNA
#$?!?
And you want to see if it exists
in any other organism

12. 13.13
BLAST
BLAST - Basic Local Alignment and Search Tool
BLAST helps you find
similarity between your
sequence and other sequences

13. 13.14
BLAST
BLAST - Basic Local Alignment and Search Tool
BLAST helps you find
similarity between your
sequence and other sequences

14. 13.15
BLAST helps you find
similarity between your
sequence and other sequences
BLAST

15. 13.16
BLAST
You can search using BLAST proteins or DNA:
Query:
DNA
Protein
Database:
DNA
Protein
blastn – nucleotides vs. nucleotides
blastp – protein vs. protein
blastx – translated query vs. protein database
tblastn– protein vs. translated nuc. DB
tblastx – translated query vs. translated database

16. 13.17
BioPerl: reading BLAST output
First we need to have the BLAST results in a text file BioPerl can read.
Here is one way to achieve this (using NCBI BLAST):
Download
Text
Another alternative is to use
BLASTALL on your computer, to
perform BLAST on each sequence of a
multiple sequence Fasta against another
multiple sequence Fasta.

17. 13.18
BioPerl: reading BLAST output
Query
Query= gi|52840257|ref|YP_094056.1| chromosomal replication initiator
protein DnaA [Legionella pneumophila subsp. pneumophila str.
Philadelphia 1]
(452 letters)
Database: Coxiella.faa
1818 sequences; 516,956 total letters
Results info
Searching..................................................done
Sequences producing significant alignments:
gi|29653365|ref|NP_819057.1|
gi|29655022|ref|NP_820714.1|
gi|29654861|ref|NP_820553.1|
gi|29654871|ref|NP_820563.1|
gi|29654481|ref|NP_820173.1|
gi|29654004|ref|NP_819696.1|
Score
E
(bits) Value
chromosomal replication initiator p...
DnaA-related protein [Coxiella burn...
Holliday junction DNA helicase B [C...
ATPase, AFG1 family [Coxiella burne...
hypothetical protein CBU_1178 [Coxi...
succinyl-diaminopimelate desuccinyl...
633
72
32
27
25
25
0.0
4e-14
0.033
1.4
3.1
3.1

18. 13.19
BioPerl: reading BLAST output
gi|215919162|ref|NP_820316.2| threonyl-tRNA synthetase [Coxiella...
gi|29655364|ref|NP_821056.1| transcription termination factor rh...
gi|215919324|ref|NP_821004.2| adenosylhomocysteinase [Coxiella b...
gi|29653813|ref|NP_819505.1| putative phosphoribosyl transferase...
25
24
24
24
5.3
9.0
9.0
9.0
Result
header
>gi|29653365|ref|NP_819057.1| chromosomal replication initiator
protein [Coxiella burnetii RSA 493]
Length = 451
Score = 633 bits (1632), Expect = 0.0
Identities = 316/452 (69%), Positives = 371/452 (82%), Gaps = 5/452 (1%)
MSTTAWQKCLGLLQDEFSAQQFNTWLRPLQAYMDEQR-LILLAPNRFVVDWVRKHFFSRI 59
+ T+ W KCLG L+DE
QQ+NTW+RPL A
+Q L+LLAPNRFV+DW+ + F +RI
LPTSLWDKCLGYLRDEIPPQQYNTWIRPLHAIESKQNGLLLLAPNRFVLDWINERFLNRI 62
Query: 1
Sbjct: 3
Query: 60
Sbjct: 63
high
scoring pair
(HSP) data
EELIKQFSGDDIKAISIEVGSKPVEAVDTPAETIVTSSSTAPLKSAPKKAVDYKSSHLNK 119
EL+ + S D
I +++GS+ E
+
+ AP
+ + +++N
TELLDELS-DTPPQIRLQIGSRSTEMPTKNSHEPSHRKAAAPPAGT---TISHTQANINS 118
HSP
Alignment
Query: 120 KFVFDSFVEGNSNQLARAASMQVAERPGDAYNPLFIYGGVGLGKTHLMHAIGNSILKNNP 179
F FDSFVEG SNQLARAA+ QVAE PG AYNPLFIYGGVGLGKTHLMHA+GN+IL+ +
Sbjct: 119 NFTFDSFVEGKSNQLARAAATQVAENPGQAYNPLFIYGGVGLGKTHLMHAVGNAILRKDS 178
Note:
There could be more than one HSP for each result,
in case of homology in different parts of the protein

19. 13.20
BioPerl installation
• In order to add BioPerl packages you need to download and
execute the bioperl10.bat file from the course website.
• If that that does not work – follow the instruction in the last
three slides of the BioPerl presentation.
• Reminder:
BioPerl warnings about:
Subroutine ... redefined at ...
Should not trouble you, it is a known issue – it is not your fault
and won't effect your script's performances.
• ftp://BioPerl.org

20. 13.21
Installing modules from the internet
• Alternatively in older Active Perl versions-
Note: ppm installs the packages under the directory “sitelib” in
the ActivePerl directory. You can put packages there manually if
you would like to download them yourself from the net, instead of
using ppm.

21. 13.22
Conclusion
Bioperl is
Powerful –
Easy –
Waiting for you (biologist) to use –

22. 13.23
Abstract Class Is...1
ABSTRACT-1
Identifying perl for DNA Blast
Author- Ostrer H
.Journal-J Exp comp •
Nov 1;290(6):567-73 2001 •
Bioperl is capable of executing analyses and processing
results from programs such as BLAST, ClustalW, or the
EMBOSS suite. Interoperation with modules written in Python
and Java is supported through the evolving BioCORBA
bridge. Bioperl provides access to data stores such as
GenBank and SwissProt via a flexible series of sequence
input/output modules, and to the emerging common sequence
. data storage format

23. 13.24
Abstract Class Is...2

24. 13.25
Abstract Class Is...3
ABSTRACT-3 •
Learning Perl programmers
JOURNAL: The American Journal of Perl programmers. (August
(2002 vol. 76 no. 2303-310
AUTHORS: PETER MOLLER AND STEFFEN LOFT •
•
The Bioperl modules have been successfully and •
repeatedly used to reduce otherwise complex tasks
to only a few lines of code. The Bioperl object
model has been proven to be flexible enough to
support enterprise-level applications such as
EnsEMBL, while maintaining an easy learning
.curve for novice Perl programmers

25. 13.26
Conclusion
Bioperl is capable of executing analyses •
and processing results from programs such
as BLAST, ClustalW, or the EMBOSS
suite. Interoperation with modules written
in Python and Java is supported through the
evolving BioCORBA bridge. Bioperl
provides access to data stores such as
GenBank and SwissProt via a flexible series
Author Affiliations: Department of Computer Science,
.(..Washington University (IanKorf et al

26. 13.27
SynopSiS
This study describes the overall architecture
of the toolkit, the problem domains that it
addresses, and gives specific examples of
how the toolkit can be used to solve
common life-sciences problems. We
conclude with a discussion of how the
open-source nature of the project has
contributed to the development effort
.Author Affiliations: Institute of Molecular and Cell
Biology, 117609 Singapore Georg Fuellen et al

27. 13.28
BOOK SOURCE :REFRENCE
Mastering perl for bio-informatics
Author : James T. Tisdal
Page No 21,22
Edition :2001
Beginning perl bio-informatics
Author: Waltr reighth
Page No: 251,253,254
Edition :2009
Developing Perl skills
Author: George keith
Page No:119
Edition :2011

28. 13.29
INTERNET :REFRENCE

29. 13.30
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