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
Read More