Lecture 13 - Biological Sequence Databases Protein Information Resource (PIR) | Bioinformatics - Botany PDF Download

 Page 1


Biological Sequence Databases   Protein Information Resource (PIR) 
 
Institute of Lifelong Learning, University of Delhi 
 
 
 
 
 
 
 
 
Subject: Bioinformatics  
Lesson: Biological Sequence Databases   Protein Information 
Resource (PIR) 
Lesson Developer: Suman Sharma 
College/ Department: Department of Botany, Ramjas College, 
University of Delhi 
  
Page 2


Biological Sequence Databases   Protein Information Resource (PIR) 
 
Institute of Lifelong Learning, University of Delhi 
 
 
 
 
 
 
 
 
Subject: Bioinformatics  
Lesson: Biological Sequence Databases   Protein Information 
Resource (PIR) 
Lesson Developer: Suman Sharma 
College/ Department: Department of Botany, Ramjas College, 
University of Delhi 
  
Protein Information Resource 
Institute of Lifelong Learning, University of Delhi 1 
 
 
Table of Contents       
 
Chapter 1: Protein Information Resource (PIR) 
? Introduction 
? Features of PIR 
o Classification 
o Non Redundancy 
o Standardized Annotation 
o Cross Reference 
o Comprehensiveness 
o Regular releases with free accessibility 
o Retrieval of information from the site 
?  Database organization and annotation 
o PIR – international sequences and auxillary database 
? PIR Resources 
o Data Retrieval system 
o Databases in PIR 
? Summary 
? Exercises 
? Glossary 
? Suggested Reading 
 
 
 
 
 
 
 
 
Page 3


Biological Sequence Databases   Protein Information Resource (PIR) 
 
Institute of Lifelong Learning, University of Delhi 
 
 
 
 
 
 
 
 
Subject: Bioinformatics  
Lesson: Biological Sequence Databases   Protein Information 
Resource (PIR) 
Lesson Developer: Suman Sharma 
College/ Department: Department of Botany, Ramjas College, 
University of Delhi 
  
Protein Information Resource 
Institute of Lifelong Learning, University of Delhi 1 
 
 
Table of Contents       
 
Chapter 1: Protein Information Resource (PIR) 
? Introduction 
? Features of PIR 
o Classification 
o Non Redundancy 
o Standardized Annotation 
o Cross Reference 
o Comprehensiveness 
o Regular releases with free accessibility 
o Retrieval of information from the site 
?  Database organization and annotation 
o PIR – international sequences and auxillary database 
? PIR Resources 
o Data Retrieval system 
o Databases in PIR 
? Summary 
? Exercises 
? Glossary 
? Suggested Reading 
 
 
 
 
 
 
 
 
Protein Information Resource 
Institute of Lifelong Learning, University of Delhi 2 
Introduction 
The rapid increase in number of genome sequencing projects has generated enormous 
amount of molecular data. In order to fully understand this huge genome base data, 
computational tools are required which can help in identification of structure, function and 
biologically relevant features in the sequences. In order to serve this purpose Protein 
Information Resource (PIR) was established to generate tools and resources for data 
storage and analysis of protein sequence for scientific community.  
In year 1984, National Biomedical Research Foundation (NBRF) developed PIR (Protein 
Information Resource) for identification and interpretation of information on protein 
sequences (http://www.nbrf.georgetown.edu/pir/find.html). This database was actually 
derived from ‘Atlas of Protein Sequence and Structure’, which was developed by Margaret O. 
Dayhoff in the year 1964. Four years later in 1988, PIR along with NBRF, Munich 
Information Centre for Protein Sequences (MIPS) and the Japan International Protein 
Information Database (JIPID), developed an organization referred as PIR – international 
with four main aims: 
(1) to create an organized, non redundant, comprehensive protein database to study 
structural, functional and evolutionary relationships  
(2) to generate information on biological origin of protein sequences  
(3) to make database easily accessible in public domain  
(4) to enable cross reference with other databases for presenting structural information of 
biomolecules. 
The Protein Information Resource (PIR) is one of the most well established databases for 
annotated protein sequences in public domain. The expanded PIR website allows not only 
sequence similarity search but also other features like text based search for protein 
sequences and cross talk with auxillary databases, annotation – sorted search, domain 
search, combined global and domain search and interactive text searches.   
 
Page 4


Biological Sequence Databases   Protein Information Resource (PIR) 
 
Institute of Lifelong Learning, University of Delhi 
 
 
 
 
 
 
 
 
Subject: Bioinformatics  
Lesson: Biological Sequence Databases   Protein Information 
Resource (PIR) 
Lesson Developer: Suman Sharma 
College/ Department: Department of Botany, Ramjas College, 
University of Delhi 
  
Protein Information Resource 
Institute of Lifelong Learning, University of Delhi 1 
 
 
Table of Contents       
 
Chapter 1: Protein Information Resource (PIR) 
? Introduction 
? Features of PIR 
o Classification 
o Non Redundancy 
o Standardized Annotation 
o Cross Reference 
o Comprehensiveness 
o Regular releases with free accessibility 
o Retrieval of information from the site 
?  Database organization and annotation 
o PIR – international sequences and auxillary database 
? PIR Resources 
o Data Retrieval system 
o Databases in PIR 
? Summary 
? Exercises 
? Glossary 
? Suggested Reading 
 
 
 
 
 
 
 
 
Protein Information Resource 
Institute of Lifelong Learning, University of Delhi 2 
Introduction 
The rapid increase in number of genome sequencing projects has generated enormous 
amount of molecular data. In order to fully understand this huge genome base data, 
computational tools are required which can help in identification of structure, function and 
biologically relevant features in the sequences. In order to serve this purpose Protein 
Information Resource (PIR) was established to generate tools and resources for data 
storage and analysis of protein sequence for scientific community.  
In year 1984, National Biomedical Research Foundation (NBRF) developed PIR (Protein 
Information Resource) for identification and interpretation of information on protein 
sequences (http://www.nbrf.georgetown.edu/pir/find.html). This database was actually 
derived from ‘Atlas of Protein Sequence and Structure’, which was developed by Margaret O. 
Dayhoff in the year 1964. Four years later in 1988, PIR along with NBRF, Munich 
Information Centre for Protein Sequences (MIPS) and the Japan International Protein 
Information Database (JIPID), developed an organization referred as PIR – international 
with four main aims: 
(1) to create an organized, non redundant, comprehensive protein database to study 
structural, functional and evolutionary relationships  
(2) to generate information on biological origin of protein sequences  
(3) to make database easily accessible in public domain  
(4) to enable cross reference with other databases for presenting structural information of 
biomolecules. 
The Protein Information Resource (PIR) is one of the most well established databases for 
annotated protein sequences in public domain. The expanded PIR website allows not only 
sequence similarity search but also other features like text based search for protein 
sequences and cross talk with auxillary databases, annotation – sorted search, domain 
search, combined global and domain search and interactive text searches.   
 
Protein Information Resource 
Institute of Lifelong Learning, University of Delhi 3 
 
Figure:  PIR  Homepage 
Source: http://pir.georgetown.edu/pirwww/ 
Features of PIR Database 
Classification :. In PIR on the basis of similarity, sequences are classified into families, 
superfamilies and homology domains. These families are organized and aligned so that 
database can be searched easily by the name of the gene family. 
Cross Reference: In PIR all entries are cross-referred to reference and molecular 
databases like Medline, Genbank, EMBL, DDBJ, Protein Data Bank, Human Genome 
Database etc so that information retrieval can be optimized. Cross referenced database 
entries are represented in form of Hypertext-links. 
Non-Redundancy: PIR is a non-redundant database; sequences from a species with 
very high identity and similarity value are merged as single entry. Even on merging identity 
of independently reported sequence is not lost and can be discretely observed from the 
canonical sequence so that the reported sequence can be reconstructed on PIR site.   
Page 5


Biological Sequence Databases   Protein Information Resource (PIR) 
 
Institute of Lifelong Learning, University of Delhi 
 
 
 
 
 
 
 
 
Subject: Bioinformatics  
Lesson: Biological Sequence Databases   Protein Information 
Resource (PIR) 
Lesson Developer: Suman Sharma 
College/ Department: Department of Botany, Ramjas College, 
University of Delhi 
  
Protein Information Resource 
Institute of Lifelong Learning, University of Delhi 1 
 
 
Table of Contents       
 
Chapter 1: Protein Information Resource (PIR) 
? Introduction 
? Features of PIR 
o Classification 
o Non Redundancy 
o Standardized Annotation 
o Cross Reference 
o Comprehensiveness 
o Regular releases with free accessibility 
o Retrieval of information from the site 
?  Database organization and annotation 
o PIR – international sequences and auxillary database 
? PIR Resources 
o Data Retrieval system 
o Databases in PIR 
? Summary 
? Exercises 
? Glossary 
? Suggested Reading 
 
 
 
 
 
 
 
 
Protein Information Resource 
Institute of Lifelong Learning, University of Delhi 2 
Introduction 
The rapid increase in number of genome sequencing projects has generated enormous 
amount of molecular data. In order to fully understand this huge genome base data, 
computational tools are required which can help in identification of structure, function and 
biologically relevant features in the sequences. In order to serve this purpose Protein 
Information Resource (PIR) was established to generate tools and resources for data 
storage and analysis of protein sequence for scientific community.  
In year 1984, National Biomedical Research Foundation (NBRF) developed PIR (Protein 
Information Resource) for identification and interpretation of information on protein 
sequences (http://www.nbrf.georgetown.edu/pir/find.html). This database was actually 
derived from ‘Atlas of Protein Sequence and Structure’, which was developed by Margaret O. 
Dayhoff in the year 1964. Four years later in 1988, PIR along with NBRF, Munich 
Information Centre for Protein Sequences (MIPS) and the Japan International Protein 
Information Database (JIPID), developed an organization referred as PIR – international 
with four main aims: 
(1) to create an organized, non redundant, comprehensive protein database to study 
structural, functional and evolutionary relationships  
(2) to generate information on biological origin of protein sequences  
(3) to make database easily accessible in public domain  
(4) to enable cross reference with other databases for presenting structural information of 
biomolecules. 
The Protein Information Resource (PIR) is one of the most well established databases for 
annotated protein sequences in public domain. The expanded PIR website allows not only 
sequence similarity search but also other features like text based search for protein 
sequences and cross talk with auxillary databases, annotation – sorted search, domain 
search, combined global and domain search and interactive text searches.   
 
Protein Information Resource 
Institute of Lifelong Learning, University of Delhi 3 
 
Figure:  PIR  Homepage 
Source: http://pir.georgetown.edu/pirwww/ 
Features of PIR Database 
Classification :. In PIR on the basis of similarity, sequences are classified into families, 
superfamilies and homology domains. These families are organized and aligned so that 
database can be searched easily by the name of the gene family. 
Cross Reference: In PIR all entries are cross-referred to reference and molecular 
databases like Medline, Genbank, EMBL, DDBJ, Protein Data Bank, Human Genome 
Database etc so that information retrieval can be optimized. Cross referenced database 
entries are represented in form of Hypertext-links. 
Non-Redundancy: PIR is a non-redundant database; sequences from a species with 
very high identity and similarity value are merged as single entry. Even on merging identity 
of independently reported sequence is not lost and can be discretely observed from the 
canonical sequence so that the reported sequence can be reconstructed on PIR site.   
Protein Information Resource 
Institute of Lifelong Learning, University of Delhi 4 
 Annotation standardized: Unlike other databases original submission entries are 
annotated at PIR. All entries have complete citations, which includes article titles, genetic 
information, mapped genes, position of introns. For high consistency and accuracy 
conserved and standardized terminologies and annotations are provided in the database 
Comprehensiveness: PIR along with other databases, which are maintained by it, 
presents the most comprehensive repository of protein sequences. 
Regular releases and free accessibility: the database is updated and released 
quarterly. Weekly updates can also be searched on PIR website. Unlike other database, 
sequences in PIR can be accessed in public domain as soon as they are received by the 
resource. 
Retrieval of information from the site: retrieval of data and knowledge is 
supported by various options like superfamilies, features, authors, keywords, and sequence 
similarity. Multiple sequence alignments and family classification supported by hypertext 
links, facilitates fast retrieval of information on related sequences either in PIR or in other 
molecular databases. 
Table : PIR web site URLs  
Tools URLs 
PIR Home page http://www.nbrf.georgetown.edu/pir/ 
MIPS Home Page http://www.mips.biochem.mpg.de/ 
Text Search http://www.nbrf.georgetown.edu/pir/find.html 
Sequence Scan http://www.nbrf.georgetown.edu/nbrf/scan.html 
Sequence 
Search 
http://www.nbrf.georgetown.edu/nbrf/search.html 
Complete 
Genome 
http://www.nbrf.georgetown.edu/pir/genome.html 
PIR Alignment 
search 
http://www.nbrf.georgetown.edu/nbrf/getaln.html