Lecture 11 - Resources at DDBJ | Bioinformatics - Botany PDF Download

 Page 1


Resources at DDBJ 
Institute of Lifelong Learning, University of Delhi 
 
 
 
 
 
 
 
  
Subject: Bioinformatic 
Lesson: Resources at DDBJ  
Lesson Developer: Jasmeet Kaur Abat 
College/ Department: Gargi College,Department of Botany, 
University of Delhi 
Page 2


Resources at DDBJ 
Institute of Lifelong Learning, University of Delhi 
 
 
 
 
 
 
 
  
Subject: Bioinformatic 
Lesson: Resources at DDBJ  
Lesson Developer: Jasmeet Kaur Abat 
College/ Department: Gargi College,Department of Botany, 
University of Delhi 
Resources at DDBJ 
Institute of Lifelong Learning, University of Delhi 1 
 
 
Table of Contents 
       
Chapter: Resources at DDBJ        
? Introduction                                              
? Tools for Database Search 
? Getentry 
? ARSA 
? TXSearch 
? Vector Screening System 
? BLAST 
? Tools for Genome Analysis 
? GIB 
? GIB-V 
? GTOP 
? MiGAP 
? Tools for Protein Database and Structure 
? LIBRA 
? PMD 
 
? Summary  
? Exercise/ Practice 
? Glossary 
? References/ Bibliography/ Further Reading 
 
 
 
 
 
 
 
 
 
Page 3


Resources at DDBJ 
Institute of Lifelong Learning, University of Delhi 
 
 
 
 
 
 
 
  
Subject: Bioinformatic 
Lesson: Resources at DDBJ  
Lesson Developer: Jasmeet Kaur Abat 
College/ Department: Gargi College,Department of Botany, 
University of Delhi 
Resources at DDBJ 
Institute of Lifelong Learning, University of Delhi 1 
 
 
Table of Contents 
       
Chapter: Resources at DDBJ        
? Introduction                                              
? Tools for Database Search 
? Getentry 
? ARSA 
? TXSearch 
? Vector Screening System 
? BLAST 
? Tools for Genome Analysis 
? GIB 
? GIB-V 
? GTOP 
? MiGAP 
? Tools for Protein Database and Structure 
? LIBRA 
? PMD 
 
? Summary  
? Exercise/ Practice 
? Glossary 
? References/ Bibliography/ Further Reading 
 
 
 
 
 
 
 
 
 
Resources at DDBJ 
Institute of Lifelong Learning, University of Delhi 2 
Introduction    
DDBJ (http://www.ddbj.nig.ac.jp ) is one of the primary nucleotide databases and hosts a 
variety of resources for data submission, retrieval and analysis. Tools for data submission 
were discussed in the previous chapter. This chapter focuses on different resources 
available at DDBJ. The resources include databases as well as the analysis tools. Various 
resources are categorized into following categories: 
? Tools for Database Search 
? Tools for Genome Analysis 
? Tools for Protein Database and structure 
 
 
 
 
 
 
 
 
 
 
Figure: Figure: Various tools at DDBJ 
Source: http://www.ddbj.nig.ac.jp/ 
Tools for Database Search 
Tools available for Database Search in DDBJ include Getentry, ARSA, TXSearch, Vector 
Screening System and BLAST. Functions of these tools are discussed as followed: 
 
Getentry 
It is a tool for quick data retrieval by use of search strings including accession number 
(http://getentry.ddbj.nig.ac.jp/top-e.html ). Data retrieval using getentry was discussed in 
the previous chapter in details. 
Page 4


Resources at DDBJ 
Institute of Lifelong Learning, University of Delhi 
 
 
 
 
 
 
 
  
Subject: Bioinformatic 
Lesson: Resources at DDBJ  
Lesson Developer: Jasmeet Kaur Abat 
College/ Department: Gargi College,Department of Botany, 
University of Delhi 
Resources at DDBJ 
Institute of Lifelong Learning, University of Delhi 1 
 
 
Table of Contents 
       
Chapter: Resources at DDBJ        
? Introduction                                              
? Tools for Database Search 
? Getentry 
? ARSA 
? TXSearch 
? Vector Screening System 
? BLAST 
? Tools for Genome Analysis 
? GIB 
? GIB-V 
? GTOP 
? MiGAP 
? Tools for Protein Database and Structure 
? LIBRA 
? PMD 
 
? Summary  
? Exercise/ Practice 
? Glossary 
? References/ Bibliography/ Further Reading 
 
 
 
 
 
 
 
 
 
Resources at DDBJ 
Institute of Lifelong Learning, University of Delhi 2 
Introduction    
DDBJ (http://www.ddbj.nig.ac.jp ) is one of the primary nucleotide databases and hosts a 
variety of resources for data submission, retrieval and analysis. Tools for data submission 
were discussed in the previous chapter. This chapter focuses on different resources 
available at DDBJ. The resources include databases as well as the analysis tools. Various 
resources are categorized into following categories: 
? Tools for Database Search 
? Tools for Genome Analysis 
? Tools for Protein Database and structure 
 
 
 
 
 
 
 
 
 
 
Figure: Figure: Various tools at DDBJ 
Source: http://www.ddbj.nig.ac.jp/ 
Tools for Database Search 
Tools available for Database Search in DDBJ include Getentry, ARSA, TXSearch, Vector 
Screening System and BLAST. Functions of these tools are discussed as followed: 
 
Getentry 
It is a tool for quick data retrieval by use of search strings including accession number 
(http://getentry.ddbj.nig.ac.jp/top-e.html ). Data retrieval using getentry was discussed in 
the previous chapter in details. 
Resources at DDBJ 
Institute of Lifelong Learning, University of Delhi 3 
 
ARSA (All-Round Retrieval of Sequence and Annotation):  
ARSA is a cross database search engine used for sequence retrieval from multiple 
databases (http://arsa.ddbj.nig.ac.jp/html/). In it any combination of features from the flat 
file format of an entry can be used as query for retrieval. Since its launch in 2004, there has 
been continuous upgradation of ARSA. Due to its frequent usage it has replaced SRS 
(Sequence Retrieval System) tool, which was earlier available at DDBJ for data retrieval by 
use of key words. NCBI also has a cross-database search and retrieval tool called as Entrez 
while EMBL has SRS with similar function. 
ARSA has two types of search options: 
? Quick Search: It involves typing a single or combination of key words in the search 
window . It is fast as compared to advanced search.  
 
 
 
 
Figure: Quick Search page of ARSA   
Source: http://arsa.ddbj.nig.ac.jp/html/ 
? Advanced Search: Advanced search is a detailed search option, which involves 
searching with help of number of parameters. Although it is more time consuming 
but it gives very accurate results. Figure 1.3 shows the advanced search page of 
ARSA. Various parameters which can be used in advanced search include gene 
name, accession number, division, sequence length, molecule type, author name etc. 
 
 
 
 
 
 
 
Page 5


Resources at DDBJ 
Institute of Lifelong Learning, University of Delhi 
 
 
 
 
 
 
 
  
Subject: Bioinformatic 
Lesson: Resources at DDBJ  
Lesson Developer: Jasmeet Kaur Abat 
College/ Department: Gargi College,Department of Botany, 
University of Delhi 
Resources at DDBJ 
Institute of Lifelong Learning, University of Delhi 1 
 
 
Table of Contents 
       
Chapter: Resources at DDBJ        
? Introduction                                              
? Tools for Database Search 
? Getentry 
? ARSA 
? TXSearch 
? Vector Screening System 
? BLAST 
? Tools for Genome Analysis 
? GIB 
? GIB-V 
? GTOP 
? MiGAP 
? Tools for Protein Database and Structure 
? LIBRA 
? PMD 
 
? Summary  
? Exercise/ Practice 
? Glossary 
? References/ Bibliography/ Further Reading 
 
 
 
 
 
 
 
 
 
Resources at DDBJ 
Institute of Lifelong Learning, University of Delhi 2 
Introduction    
DDBJ (http://www.ddbj.nig.ac.jp ) is one of the primary nucleotide databases and hosts a 
variety of resources for data submission, retrieval and analysis. Tools for data submission 
were discussed in the previous chapter. This chapter focuses on different resources 
available at DDBJ. The resources include databases as well as the analysis tools. Various 
resources are categorized into following categories: 
? Tools for Database Search 
? Tools for Genome Analysis 
? Tools for Protein Database and structure 
 
 
 
 
 
 
 
 
 
 
Figure: Figure: Various tools at DDBJ 
Source: http://www.ddbj.nig.ac.jp/ 
Tools for Database Search 
Tools available for Database Search in DDBJ include Getentry, ARSA, TXSearch, Vector 
Screening System and BLAST. Functions of these tools are discussed as followed: 
 
Getentry 
It is a tool for quick data retrieval by use of search strings including accession number 
(http://getentry.ddbj.nig.ac.jp/top-e.html ). Data retrieval using getentry was discussed in 
the previous chapter in details. 
Resources at DDBJ 
Institute of Lifelong Learning, University of Delhi 3 
 
ARSA (All-Round Retrieval of Sequence and Annotation):  
ARSA is a cross database search engine used for sequence retrieval from multiple 
databases (http://arsa.ddbj.nig.ac.jp/html/). In it any combination of features from the flat 
file format of an entry can be used as query for retrieval. Since its launch in 2004, there has 
been continuous upgradation of ARSA. Due to its frequent usage it has replaced SRS 
(Sequence Retrieval System) tool, which was earlier available at DDBJ for data retrieval by 
use of key words. NCBI also has a cross-database search and retrieval tool called as Entrez 
while EMBL has SRS with similar function. 
ARSA has two types of search options: 
? Quick Search: It involves typing a single or combination of key words in the search 
window . It is fast as compared to advanced search.  
 
 
 
 
Figure: Quick Search page of ARSA   
Source: http://arsa.ddbj.nig.ac.jp/html/ 
? Advanced Search: Advanced search is a detailed search option, which involves 
searching with help of number of parameters. Although it is more time consuming 
but it gives very accurate results. Figure 1.3 shows the advanced search page of 
ARSA. Various parameters which can be used in advanced search include gene 
name, accession number, division, sequence length, molecule type, author name etc. 
 
 
 
 
 
 
 
Resources at DDBJ 
Institute of Lifelong Learning, University of Delhi 4 
 
Figure:  Advanced Search page of ARSA   
Source: http://arsa.ddbj.nig.ac.jp/html/AdvancedSearchMenu 
TXSearch (Taxonomy Search):  
Taxonomy search is a retrieval tool for Taxonomy database (integrated by DDBJ, GenBank 
and EMBL) and aim of this tool is to amalgamate organism names 
(http://txsearch.ddbj.nig.ac.jp/top-e.html). It is used for searching unified taxonomy 
names. This information is required during submission of nucleotide sequence where 
complete taxonomic classification of the organism is needed. The search can be done by 
using Taxonomic name, ID, class or rank. Taxonomic classification of Brassica juncea 
retrieved using TXSearch is shown in Figure. 
 
 
 
 
 
 
 
 
 
 
 
 
 
Figure: Taxonomy Search page of DDBJ  
Source: http://txsearch.ddbj.nig.ac.jp/top-e.html 
Vector Screening System (VSS):  
In Recombinant DNA technology (for cloning, over-expression or transformation), PCR 
amplified genomic DNA or complementary DNA (cDNA) is inserted into a vector. During 
sequencing, the sequence of the cloned DNA (genomic or cDNA) segment usually gets 
contaminated by the vector sequence. Therefore it becomes necessary to recognize and 
remove vector sequence from the DNA sequence otherwise it may lead to wrong conclusion 
about the results obtained. 
Vector Screening system (http://vector.ddbj.nig.ac.jp/top-e.html ) as the name suggests is 
used for detection of vector sequence contamination in the query sequence. It uses a target 
Complete taxonomic 
lineage of Brassica juncea