Podcast
Questions and Answers
The term Bioinformatics was first coined by Paulien Hogeweg and Ben ______________ in 1960.
The term Bioinformatics was first coined by Paulien Hogeweg and Ben ______________ in 1960.
Hesper
The unique ring structure of ______________ can impact protein folding and stability.
The unique ring structure of ______________ can impact protein folding and stability.
Proline
The simplicity and flexibility of ______________ make it a crucial component of protein structures.
The simplicity and flexibility of ______________ make it a crucial component of protein structures.
Glycine
The ability of ______________ to form disulfide bonds is essential for protein structure stabilization.
The ability of ______________ to form disulfide bonds is essential for protein structure stabilization.
The amphoteric nature and ability to switch between protonation states make ______________ a crucial player in enzyme catalysis and protein function.
The amphoteric nature and ability to switch between protonation states make ______________ a crucial player in enzyme catalysis and protein function.
Data is raw, unorganized ______ need to be processed.
Data is raw, unorganized ______ need to be processed.
When data is processed, organized, structured or presented in a given context so as to make it useful it is called ______.
When data is processed, organized, structured or presented in a given context so as to make it useful it is called ______.
Primary Databases contain ______ data in its original form.
Primary Databases contain ______ data in its original form.
Experimental results are submitted directly into the ______ by researchers, and the data are essentially archival in nature.
Experimental results are submitted directly into the ______ by researchers, and the data are essentially archival in nature.
GenBank is a ______ from NCBI, includes sequences from publically available resources.
GenBank is a ______ from NCBI, includes sequences from publically available resources.
EMBL is a ______ acid Database that comes under EBI.
EMBL is a ______ acid Database that comes under EBI.
DDBJ is a biological ______ that collects DNA Sequences.
DDBJ is a biological ______ that collects DNA Sequences.
DDBJ is located at the National Institute of Genetics in the ______ Prefecture of Japan.
DDBJ is located at the National Institute of Genetics in the ______ Prefecture of Japan.
SWISS – PROT is a curated ______________ sequence database which strives to provide a high level of annotation.
SWISS – PROT is a curated ______________ sequence database which strives to provide a high level of annotation.
The Protein Information Resources (PIR) maintains the ______________ Sequence Database (PSD), an annotated protein database containing over 283000 sequences.
The Protein Information Resources (PIR) maintains the ______________ Sequence Database (PSD), an annotated protein database containing over 283000 sequences.
PROSITE is a protein database that consists of entries describing the protein ______________ , domains and functional sites as well as amino acid patterns and profiles in them.
PROSITE is a protein database that consists of entries describing the protein ______________ , domains and functional sites as well as amino acid patterns and profiles in them.
Pfam is a database of ______________ families that includes their annotations and multiple alignments generated using hidden markov models.
Pfam is a database of ______________ families that includes their annotations and multiple alignments generated using hidden markov models.
The general purpose of the pfam database is to provide a complete and accurate classification of ______________ families and domains.
The general purpose of the pfam database is to provide a complete and accurate classification of ______________ families and domains.
PDB (protein data bank) comprises of : 1.PDBe ( PDB of ______________ ) and 2.PDBj ( PDB of ______________ ).
PDB (protein data bank) comprises of : 1.PDBe ( PDB of ______________ ) and 2.PDBj ( PDB of ______________ ).
SCOPE is a database that provides a structural classification of ______________.
SCOPE is a database that provides a structural classification of ______________.
CATH is a database that provides a classification of protein structures based on ______________, Architecture, Topology, and Homology.
CATH is a database that provides a classification of protein structures based on ______________, Architecture, Topology, and Homology.
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Study Notes
Bioinformatics
- Bioinformatics is a crucial field that combines computational tools and biological data to analyze and understand biological systems.
History of Bioinformatics
- The term "bioinformatics" was first coined by Paulien Hogeweg and Ben Hesper in 1960.
Special Cases of Amino Acids
- Proline (Pro): Has a unique ring structure that can impact protein folding and stability.
- Glycine (Gly): Is a crucial component of protein structures due to its simplicity and flexibility.
- Cysteine (Cys): Forms disulfide bonds that are essential for protein structure stabilization.
- Histidine: Has an amphoteric nature and can switch between protonation states, making it crucial for enzyme catalysis and protein function.
Importance of Amino Acids
- Amino acids play diverse and essential roles in protein structure, function, and overall biological processes.
Data and Information
- Data is raw, unorganized facts that need to be processed.
- Information is processed, organized, structured, or presented in a given context to make it useful.
Biological Databases
- Classified into two types based on the nature of data and source.
Primary Databases
- Contain biomolecular data in its original form.
- Experimental results are submitted directly into the database by researchers.
- Data is essentially archival in nature and cannot be changed further once a database accession number is assigned.
- Examples: GenBank, EMBL, DDBJ for DNA/RNA sequences, and SWISS-PROT and PIR for protein sequences.
GenBank
- A database from NCBI that includes sequences from publicly available resources.
- A genetic sequence database, an annotated collection of all publicly available DNA sequences.
- Part of the International Nucleotide Sequence Database Collaboration.
EMBL
- European Molecular Biological Laboratory, a nucleic acid database that comes under EBI (European Bioinformatics Institute).
- Established in collaboration with DDBJ and GenBank.
- EBI's Sequence Retrieval System (SRS) is a network browser for databanks in molecular biology.
DDBJ
- The DNA Data Bank of Japan, a biological database that collects DNA sequences.
- Located at the National Institute of Genetics in Japan.
- A member of the International Nucleotide Sequence Database Collaboration or INSDC.
SWISS-PROT
- A curated protein sequence database that provides high-level annotation.
- Annotations include description of protein function, domains, post-translational modifications, variants, etc.
- Created in 1986 by Amos Bairoch with Swiss Institute of Bioinformatics.
PIR
- The Protein Information Resources (PIR) is an integrated public resource of protein informatics.
- Supports genomic and proteomic research and scientific discovery.
- Maintains the Protein Sequence Database (PSD), an annotated protein database containing over 283,000 sequences.
Secondary Database
- Contains data derived from analyzed primary data.
- Data is either manually created or generated automatically.
- Contains valuable information such as about mutations or evolutionary relationships.
- Examples: PROSITE, Pfam.
PROSITE
- A protein database that consists of entries describing protein families, domains, and functional sites.
- Manually curated by a team of the Swiss Institute of Bioinformatics.
- Tightly integrated into Swiss-Prot protein annotation.
Pfam
- A database of protein families that includes their annotations and multiple alignments generated using hidden Markov models.
- Provides a complete and accurate classification of protein families and domains.
Structural Database
- PDB (Protein Data Bank): comprises of PDBe (PDB of Europe), PDBj (PDB of Japan), SCOPE, and CATH.
- Contains information generated from X-Crystallgraphy and NMR Experiments.
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