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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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13.1 Pearl and Biopearl TOOLS FOR BIOINFORMATICS
Pearl and Biopearl TOOLS FOR BIOINFORMATICS
SUBMITTED BY :AAMIR JAVED
MSc 1ST SEM REG NO :11CQST2001
SUBMITTED TO : DR T.S.MURALIDHAR
HOD OF BIOTECHNOLOGY
13.2
בשבועות הקרובים יתקיים סקר
ההוראה(
באתר מידע אישילתלמיד
)
סקר הוראה
13.3
CONTENTS• Introduction• Bio pearl modules• What is Perl ?• Why use Perl ?• What’s bioperl ? • Why bioperl for bioinformatics• Things we can do with bioperl• Conclusion• Abstract• Synopsis• Reference
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 molecular biological data.
Background:Started in 1995One of the oldest open source Bioinformatics
Toolkit Projecthttp://bugzilla.BioPerl.org/
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.
13.8
Why use Perl?
Easy to use
Fast
Portability
Efficiency
Free to use
Correctness
13.9
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.
What’s BioPerl
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
13.11
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.
We will not learn object oriented programming,
but we will learn how to create and use objects defined by BioPerl packages.
Object-oriented use of packages
$obj0x225d14
func)(anotherFunc)(
13.12BLAST
Congrats, you just sequenced yourself some DNA.
And you want to see if it exists in any other organism#$?!?
13.13
BLAST
BLAST helps you find similarity between your
sequence and other sequences
BLAST - Basic Local Alignment and Search Tool
13.14
BLAST
BLAST helps you find similarity between your
sequence and other sequences
BLAST - Basic Local Alignment and Search Tool
13.15
BLAST
BLAST helps you find similarity between your
sequence and other sequences
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BLAST
Query: DNA Protein
Database: DNA Protein
blastn – nucleotides vs. nucleotidesblastp – protein vs. protein
blastx – translated query vs. protein database
tblastn– protein vs. translated nuc. DB
tblastx– translated query vs. translated database
You can search using BLAST proteins or DNA:
13.17
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):
BioPerl: reading BLAST output
Text
Download
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.
13.18
Query= gi|52840257|ref|YP_094056.1| chromosomal replication initiatorprotein DnaA [Legionella pneumophila subsp. pneumophila str.Philadelphia 1] )452 letters(
Database: Coxiella.faa 1818 sequences; 516,956 total letters
Searching..................................................done
Score ESequences producing significant alignments: )bits( Value
gi|29653365|ref|NP_819057.1| chromosomal replication initiator p... 633 0.0 gi|29655022|ref|NP_820714.1| DnaA-related protein [Coxiella burn... 72 4e-14gi|29654861|ref|NP_820553.1| Holliday junction DNA helicase B [C... 32 0.033gi|29654871|ref|NP_820563.1| ATPase, AFG1 family [Coxiella burne... 27 1.4 gi|29654481|ref|NP_820173.1| hypothetical protein CBU_1178 [Coxi... 25 3.1 gi|29654004|ref|NP_819696.1| succinyl-diaminopimelate desuccinyl... 25 3.1
BioPerl: reading BLAST outputQuery
Results info
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gi|215919162|ref|NP_820316.2| threonyl-tRNA synthetase [Coxiella... 25 5.3 gi|29655364|ref|NP_821056.1| transcription termination factor rh... 24 9.0 gi|215919324|ref|NP_821004.2| adenosylhomocysteinase [Coxiella b... 24 9.0 gi|29653813|ref|NP_819505.1| putative phosphoribosyl transferase... 24 9.0
>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%(
Query: 1 MSTTAWQKCLGLLQDEFSAQQFNTWLRPLQAYMDEQR-LILLAPNRFVVDWVRKHFFSRI 59 + T+ W KCLG L+DE QQ+NTW+RPL A +Q L+LLAPNRFV+DW+ + F +RISbjct: 3 LPTSLWDKCLGYLRDEIPPQQYNTWIRPLHAIESKQNGLLLLAPNRFVLDWINERFLNRI 62
Query: 60 EELIKQFSGDDIKAISIEVGSKPVEAVDTPAETIVTSSSTAPLKSAPKKAVDYKSSHLNK 119 EL+ + S D I +++GS+ E + + AP + + +++N Sbjct: 63 TELLDELS-DTPPQIRLQIGSRSTEMPTKNSHEPSHRKAAAPPAGT---TISHTQANINS 118
Query: 120 KFVFDSFVEGNSNQLARAASMQVAERPGDAYNPLFIYGGVGLGKTHLMHAIGNSILKNNP 179 F FDSFVEG SNQLARAA+ QVAE PG AYNPLFIYGGVGLGKTHLMHA+GN+IL+ + Sbjct: 119 NFTFDSFVEGKSNQLARAAATQVAENPGQAYNPLFIYGGVGLGKTHLMHAVGNAILRKDS 178
BioPerl: reading BLAST output
Result header
high scoring pair (HSP) data
HSP Alignment
Note: There could be more than one HSP for each result,
in case of homology in different parts of the protein
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
13.21Installing modules from the internet
• Alternatively in older Active Perl versions-
Note: ppm installs the packages under the directory “site\lib\” 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.
13.22
Conclusion
Bioperl is–Powerful
– Easy–Waiting for you (biologist) to use
13.23
Abstract Class Is...1
ABSTRACT-1Identifying perl for DNA BlastIdentifying perl for DNA BlastAuthor- Ostrer H
•Journal-J Exp comp. •2001 Nov 1;290(6):567-73
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 .
13.24
Abstract Class Is...2
13.25
Abstract Class Is...3
•ABSTRACT-3Learning 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.
13.26Conclusion
•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...)
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
13.28BOOK 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
13.29INTERNET :REFRENCE
13.30
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