BIOINFORMATICS FOR PHARMACY
PBI20101P
LAB REPORT 1
,Experiment 1: Biological Databases with Reference to NCBI
Aim:
To view and use the various biological databases available on the World Wide Web.
Introduction:
The production of vast volumes of raw sequence data is one of the hallmarks of contemporary
genomic science. To handle the data deluge, sophisticated analytical methodologies are needed
as the amount of genomic data expands. As a result, the first task in the genomics era is to create
and use computer databases to store and manage massive amounts of data. A biological database
is a massive, well-organized collection of data that is structured, searchable, updated
periodically, and cross-referenced. The main goal of database development is to assemble data
into a series of organized documents so that information can be retrieved quickly. GenBank
from NCBI (National Center for Biotechnology Information), SwissProt from the Swiss Institute
of Bioinformatics (Swiss Institute of Bioinformatics), and PIR from the Protein Information
Resource (Protein Information Resource) are among the three common databases.
Based on source, biological databases can be divided into two categories: primary databases
and secondary databases.
Primary databases are known as archival databases. They are filled with data obtained
from experiments, such as nucleotide sequences, protein sequences, and macromolecular
structures. Researches enter experimental results directly into the database, and the evidence is
archival in nature. The data in primary databases are never updated once it has been assigned a
database accession number as it becomes part of the scientific record. Examples include
GenBank, EMBL, DDBJ for DNA/RNA sequences, SWISS-PROT, and PIR for protein
sequences.
GenBank is a database maintained by the National Center for Biotechnology Information
(NCBI) that contains DNA sequences from publicly accessible sources.EMBL stands for
European Molecular Biological Laboratory. It is a Nucleic Acid Database that comes under EBI
(European Bioinformatics Institute). EBI’s Sequence Retrieval System (SRS) is a network
browser for databanks in molecular biology, integrating and linking the main nucleotide and
protein databases. The DDBJ (DNA Data Bank of Japan) is a biological database that collects
DNA sequences. It is located at the National Institute of Genetics in the Shizuoka Prefecture of
Japan. SWISS-PORT is a curated protein sequence database that aims for high annotation
quality (such as a description of the function of proteins, its domain structure, post-translational
modifications, variants, etc.). It was created in 1986 by Amos Bairoch with the Swiss Institute of
Bioinformatics. The Protein Information Resources (PIR) is a public protein informatics
resource that promotes genomic and proteomic research as well as scientific exploration. It
, maintains the Protein Sequence Database (PSD), an annotated protein database containing over
283000 sequences covering the entire taxonomic range.
Secondary databases contain information extracted from the analysis of primary data.
Secondary databases also use data from a variety of sources, including primary and secondary
databases, managed vocabularies, and scientific literature. They are highly curated, with new
information derived from the public record of science using a complex combination of
computational algorithms and manual study and interpretation. Examples include PROSITE,
Pfam, BLOCKS and PRINTS.
PROSITE is a protein database. It includes descriptions of protein families, domains, and
functional sites, as well as amino acid patterns and profiles. They are manually created by a
team from the Swiss Institute of Bioinformatics and closely incorporated into the Swiss-Prot
protein annotation system. Pfam is a protein family database that includes annotations and
multiple alignments created by hidden Markov models. The Pfam database’s main goal is to
provide an accurate and comprehensive classification of protein families and domains.
Many data sources, on the other hand, have both primary and secondary features. Primary
sequences obtained from peptide sequencing studies, for example, are accepted by UniProt.
UniProt, on the other hand, infers peptide sequences from genomic data and offers a wealth of
additional data, some of which is derived from automated annotation (TrEMBL) and even more
from careful manual research (SwissProt).
There are also specialized databases, which cater to a specific study area. Flybase, HIV
sequence database, and Ribosomal Database Project, for example, are databases that
specialize in a specific organism or form of data.
PBI20101P
LAB REPORT 1
,Experiment 1: Biological Databases with Reference to NCBI
Aim:
To view and use the various biological databases available on the World Wide Web.
Introduction:
The production of vast volumes of raw sequence data is one of the hallmarks of contemporary
genomic science. To handle the data deluge, sophisticated analytical methodologies are needed
as the amount of genomic data expands. As a result, the first task in the genomics era is to create
and use computer databases to store and manage massive amounts of data. A biological database
is a massive, well-organized collection of data that is structured, searchable, updated
periodically, and cross-referenced. The main goal of database development is to assemble data
into a series of organized documents so that information can be retrieved quickly. GenBank
from NCBI (National Center for Biotechnology Information), SwissProt from the Swiss Institute
of Bioinformatics (Swiss Institute of Bioinformatics), and PIR from the Protein Information
Resource (Protein Information Resource) are among the three common databases.
Based on source, biological databases can be divided into two categories: primary databases
and secondary databases.
Primary databases are known as archival databases. They are filled with data obtained
from experiments, such as nucleotide sequences, protein sequences, and macromolecular
structures. Researches enter experimental results directly into the database, and the evidence is
archival in nature. The data in primary databases are never updated once it has been assigned a
database accession number as it becomes part of the scientific record. Examples include
GenBank, EMBL, DDBJ for DNA/RNA sequences, SWISS-PROT, and PIR for protein
sequences.
GenBank is a database maintained by the National Center for Biotechnology Information
(NCBI) that contains DNA sequences from publicly accessible sources.EMBL stands for
European Molecular Biological Laboratory. It is a Nucleic Acid Database that comes under EBI
(European Bioinformatics Institute). EBI’s Sequence Retrieval System (SRS) is a network
browser for databanks in molecular biology, integrating and linking the main nucleotide and
protein databases. The DDBJ (DNA Data Bank of Japan) is a biological database that collects
DNA sequences. It is located at the National Institute of Genetics in the Shizuoka Prefecture of
Japan. SWISS-PORT is a curated protein sequence database that aims for high annotation
quality (such as a description of the function of proteins, its domain structure, post-translational
modifications, variants, etc.). It was created in 1986 by Amos Bairoch with the Swiss Institute of
Bioinformatics. The Protein Information Resources (PIR) is a public protein informatics
resource that promotes genomic and proteomic research as well as scientific exploration. It
, maintains the Protein Sequence Database (PSD), an annotated protein database containing over
283000 sequences covering the entire taxonomic range.
Secondary databases contain information extracted from the analysis of primary data.
Secondary databases also use data from a variety of sources, including primary and secondary
databases, managed vocabularies, and scientific literature. They are highly curated, with new
information derived from the public record of science using a complex combination of
computational algorithms and manual study and interpretation. Examples include PROSITE,
Pfam, BLOCKS and PRINTS.
PROSITE is a protein database. It includes descriptions of protein families, domains, and
functional sites, as well as amino acid patterns and profiles. They are manually created by a
team from the Swiss Institute of Bioinformatics and closely incorporated into the Swiss-Prot
protein annotation system. Pfam is a protein family database that includes annotations and
multiple alignments created by hidden Markov models. The Pfam database’s main goal is to
provide an accurate and comprehensive classification of protein families and domains.
Many data sources, on the other hand, have both primary and secondary features. Primary
sequences obtained from peptide sequencing studies, for example, are accepted by UniProt.
UniProt, on the other hand, infers peptide sequences from genomic data and offers a wealth of
additional data, some of which is derived from automated annotation (TrEMBL) and even more
from careful manual research (SwissProt).
There are also specialized databases, which cater to a specific study area. Flybase, HIV
sequence database, and Ribosomal Database Project, for example, are databases that
specialize in a specific organism or form of data.
