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UniProt SwissProt

Bioinformatics is the application of informatics techniques to understand and organize biological information. It involves conceptualizing biology at the macromolecular level, especially regarding proteins and DNA. Key databases for protein sequence data include UniProt, Swiss-Prot, and TrEMBL. Swiss-Prot contains manually annotated and verified protein sequences. These databases allow researchers to search for protein information like sequence, function, taxonomy, and annotations. Protein structure can be analyzed at the primary, secondary, tertiary, and quaternary levels. Databases like PDB provide structural data that give insights into protein function and how mutations may cause disease.

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Ariane Benina
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22 views

UniProt SwissProt

Bioinformatics is the application of informatics techniques to understand and organize biological information. It involves conceptualizing biology at the macromolecular level, especially regarding proteins and DNA. Key databases for protein sequence data include UniProt, Swiss-Prot, and TrEMBL. Swiss-Prot contains manually annotated and verified protein sequences. These databases allow researchers to search for protein information like sequence, function, taxonomy, and annotations. Protein structure can be analyzed at the primary, secondary, tertiary, and quaternary levels. Databases like PDB provide structural data that give insights into protein function and how mutations may cause disease.

Uploaded by

Ariane Benina
Copyright
© © All Rights Reserved
Available Formats
Download as DOCX, PDF, TXT or read online on Scribd
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Bioinformatics

Conceptualizing biology in terms of macromolecules and applying “informatics” techniques


to understand and organize information associated with these molecules.

Started a
UniProt & SwissProt

 For protein sequences


 Beda UniProt sama SwissProt: Manually and annotated version of UniProt
 Two ways to sequence the protein, bisa sequence protein apa saja:
o Mass Spectrum Method:
o Admin Degradation (?) Method:
 Setelah di sequence > output ke database > bisa dilihat sama orang lain (database)
digunakan untuk penelitian yang lain.
 Database bisa dilihat dari EBI (Europena Bioinformatics Institute) bioinformatics
database di dunia.
o Bisa cari gene

UNIPROT
 Proteomes: for different organisms
 Swiss-prot (automaticly verified protein sequence 549ribu sequence) & TrEMBL
(more sequences), manually verified set of sequences

Study with protein sequences, uniport useful, for human annotated sequences ke
SwissProt
SWISSPROT
Each entry in SWISS-PROT contains the following information: Known protein
sequences, references, taxonomic information, annotations, etc.
The protein entry contains a total of 14 topics.
You can use this database to query some information you need:
 Query for aliases of target proteins
 Query the subcellular localization of protein
 Query for post-translational modifications of proteins
 Query the amino acid sequence of the protein
 Query the expected molecular weight of the protein
 Query for different possible isoforms

1. Search swissprot database (https://www.expasy.org/resources/uniprotkb-swiss-


prot)
2. Search e.g. protein myosin
3. Cara reduce > click on Fields > Protein Name [DE] > myosin (untuk cari protein yang
benr2 hanya myosin di Namanya)
4. Reduce lagi (only human) > term ketik homo sapiens > search trus keluar
5. Untuk pilih, protein names terus klik link di accession
6. Bagian sequence > references buat artikel
7. FASTA > dapet FASTA format, di copy, di analyze software lain
8. Tools > pencet menu > buat liat software lain > Blast untuk cari similar protein > go.
PROTEIN STRUCTURE (https://www.youtube.com/watch?
v=RkuvqFfNAis&ab_channel=Bio-Informatics-IITM)
 Primary structure (amino acid sequence), secondary structure (alpha helix,
beta strand), tertiary structure (3D structure w/ atomic details), quaternary
structure (assembled subunits)
o PRIMARY STRUCTURES:
 Arrangement different amino acid residue
o SECONDARY STRUTURES: kasih bentuk
o TERTIARY: location of each atom, ada xyz coordinate
 2 structures di antara: super-secondary structures (kombinasi dari berbeda
secondary structures + domain ada residu (bisa fold and perform functions
called domains)
 20 naturally occurring amino acids just like 26 alphabets >> ada beberapa
structure yang bisa
 Main Chain: beads nya berbeda (side chains)
 Small change in a protein > may lead to disease
 Primary Structures gives the linear sequence of amino acid residues, Includes
covalent bonds between amino acids (elimination of water molecule >
peptide bond). Have relative arrangement of the linked amino acids is not
specified.
 Margaret Dayhoff collected sequences of various proteins and published
contains sequences of proteins > converted to database > Protein
Information Resource (EXprot, Munich Information Center for Protein
Sequencs (MIPS), NCBI, PIR, PIR-NREF, PRF, SWISS-PROT (2 types: one
manually curreted sequenes), UNIPROT
 Average sequence length: 315 amino acids
o Most frequent residues: Leucine, Alanine, Glycine

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