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Bioinformatics. Ayesha M. Khan 22 Feb, 2012. Flowchart of sequence data from labs and literature to primary sequence database and subsequent secondary databases. Secondary Sequence Database Protein Domains & Families Metabolic Pathways

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Bioinformatics

Bioinformatics

Ayesha M. Khan

22 Feb, 2012

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Flowchart of sequence data from labs and literature to primary sequence database and subsequent secondary databases

Secondary Sequence Database

Protein Domains & Families

Metabolic Pathways

e.g. RefSeq and Conserved Domain Database (CDD) within NCBI

Primary Sequence Database

Amino AcidNucleic Acid

e.g. GenBank, EMBL, DDBJ

SwissProt and PIR

Sequencing centers

Literature

Researchers

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Always remember that: primary sequence database and subsequent secondary databases

  • The data within primary databases is as reliable as the data submitted.

  • This depends primarily on the methods used to produce it.

  • Regardless of who obtains the sequence data, nucleic acid and amino acid sequencing results are subject to errors.

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Protein sequence databases
Protein Sequence databases primary sequence database and subsequent secondary databases

  • The protein sequence database was developed at the National Biomedical Research Foundation (NBRF)

  • Early 1960’s by Margaret Dayhoff to investigate evolutionary relationships among proteins

  • 1988 onwards, maintained collectively by: Protein Information Resource (PIR) at NBRF, International Protein Information Database of Japan (JIPID), and the Martinsried Institute for Protein Sequences (MIPS).

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Examples of molecular sequence types in ncbi records
Examples of molecular sequence types in NCBI records primary sequence database and subsequent secondary databases

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Lec-4 primary sequence database and subsequent secondary databases


Lec-4 primary sequence database and subsequent secondary databases


Lec-4 primary sequence database and subsequent secondary databases


Protein sequence databases1
Protein Sequence databases primary sequence database and subsequent secondary databases

SWISS-PROT

Started in 1986-University of Geneva and EMBL

It is now maintained by Swiss Institute of Bioinformatics (SIB) and EBI/EMBL

TrEMBL

Started in 1996-Follows SWISS-PROT format and contains translations of coding sequences in EMBL.

It also provides: synthetic sequences, short amino acid fragments, and codons that do not encode real proteins.

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Composite protein sequence databases
Composite protein sequence databases primary sequence database and subsequent secondary databases

  • A database that merges a variety of different primary sources.

  • They obviate the need to interrogate multiple resources.

  • It can eliminate identical sequence copies, or eliminate both identical and highly similar sequences.

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