13.1

Pearl and Biopearl
Pearl and Biopearl
TOOLS FOR BIOINFORMATICS
TOOLS FOR BIOINFORMATICS

SUBMITTED BY :AAMIR
JAVED
M...
‫סקר הוראה‬
‫בשבועות הקרובים‬
‫יתקיים סקר‬
‫ההוראה‬
‫)‬
‫מידע אישי לתלמיד‬
‫(‬

‫2.31‬
13.3

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CONTENTS

IntroductIon
BIo pearl modules
What Is perl ?
Why use perl ?
What’s BIoperl ?
Why B...
13.5

Introduction
Perl stands for Practical Extraction •
and Report Language •

(Author: Larry Wall (1986 •
13.6

: Objective of BioPerl

 Develop

reusable, extensible core Perl modules
for use as a standard for manipulating
mol...
13.7

?What is Perl
Perl is an interpreted programming language that •
resembles both a real programming language and
.a s...
13.8

?Why use Perl
Easy to use
Fast
Portability
Efficiency
Free to use

Correctness
13.9

What’s BioPerl

The BioPerl project is an international association of developers of
open source Perl tools for bioi...
13.10

Why Bioperl for Bio-informatics?

Perl is good at file manipulation and text
processing, which make up a large part...
13.11

Object-oriented use of packages

Many packages are meant to be used as objects.
In Perl, an object is a data struct...
13.12

BLAST
Congrats, you just sequenced
.yourself some DNA

#$?!?

And you want to see if it exists
in any other organ...
13.13

BLAST

BLAST - Basic Local Alignment and Search Tool

BLAST helps you find
similarity between your
sequence and oth...
13.14

BLAST

BLAST - Basic Local Alignment and Search Tool

BLAST helps you find
similarity between your
sequence and oth...
13.15

BLAST helps you find
similarity between your
sequence and other sequences

BLAST
13.16

BLAST

You can search using BLAST proteins or DNA:
Query:

DNA

Protein

Database:

DNA

Protein

blastn – nucleoti...
13.17

BioPerl: reading BLAST output

First we need to have the BLAST results in a text file BioPerl can read.
Here is one...
13.18

BioPerl: reading BLAST output
Query

Query= gi|52840257|ref|YP_094056.1| chromosomal replication initiator
protein ...
13.19

BioPerl: reading BLAST output

gi|215919162|ref|NP_820316.2| threonyl-tRNA synthetase [Coxiella...
gi|29655364|ref|...
13.20

BioPerl installation
• In order to add BioPerl packages you need to download and
execute the bioperl10.bat file fro...
13.21

Installing modules from the internet

• Alternatively in older Active Perl versions-

Note: ppm installs the packag...
13.22

Conclusion

Bioperl is
Powerful –
Easy –
Waiting for you (biologist) to use –
13.23

Abstract Class Is...1

ABSTRACT-1
Identifying perl for DNA Blast
Author- Ostrer H
.Journal-J Exp comp •
Nov 1;290(6...
13.24

Abstract Class Is...2
13.25

Abstract Class Is...3

ABSTRACT-3 •
Learning Perl programmers
JOURNAL: The American Journal of Perl programmers. (A...
13.26

Conclusion
Bioperl is capable of executing analyses •
and processing results from programs such
as BLAST, ClustalW,...
13.27

SynopSiS
This study describes the overall architecture
of the toolkit, the problem domains that it
addresses, and g...
13.28

BOOK SOURCE :REFRENCE
Mastering perl for bio-informatics
 Author : James T. Tisdal
 Page No 21,22
Edition :2001
Beg...
13.29

INTERNET :REFRENCE
13.30

.

 
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Aamir javed perl

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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.

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Aamir javed perl

  1. 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. 2. ‫סקר הוראה‬ ‫בשבועות הקרובים‬ ‫יתקיים סקר‬ ‫ההוראה‬ ‫)‬ ‫מידע אישי לתלמיד‬ ‫(‬ ‫2.31‬
  3. 3. 13.3 • • • • • • • • • • • 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. 4. 13.5 Introduction Perl stands for Practical Extraction • and Report Language • (Author: Larry Wall (1986 •
  5. 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. 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. 7. 13.8 ?Why use Perl Easy to use Fast Portability Efficiency Free to use Correctness
  8. 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. 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. 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. 11. 13.12 BLAST Congrats, you just sequenced .yourself some DNA #$?!? And you want to see if it exists in any other organism
  12. 12. 13.13 BLAST BLAST - Basic Local Alignment and Search Tool BLAST helps you find similarity between your sequence and other sequences
  13. 13. 13.14 BLAST BLAST - Basic Local Alignment and Search Tool BLAST helps you find similarity between your sequence and other sequences
  14. 14. 13.15 BLAST helps you find similarity between your sequence and other sequences BLAST
  15. 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. 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. 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. 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. 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. 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. 21. 13.22 Conclusion Bioperl is Powerful – Easy – Waiting for you (biologist) to use –
  22. 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. 23. 13.24 Abstract Class Is...2
  24. 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. 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. 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. 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. 28. 13.29 INTERNET :REFRENCE
  29. 29. 13.30 .  

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