Sequence Databases

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Sequence Databases
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• 1.1 Introduction
• 1.2 Primary and Secondary Databases
• 1.3 Nucleotide Sequence Databases
• 1.4 Nucleotide Sequence Flatfiles
• A Dissection
• 1.5 Protein Sequence Databases
• 1.6 Summary

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1.1 Introduction

• The history of sequence databases began in the
  early 1960s, when Margaret Dayhoff and colleagues
  at the Protein Information Resource (PIR)
  collected all of the protein sequences known at
  that time.
• The advance of DNA sequence databases in 1982,
  initiated by the European Molecular biology
  Laboratory (EMBL), and joined shortly thereafter
  by GenBank.

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• The DNA Databank of Japan (DDBJ) joined the
  data-collecting collaboration a few years later.
• DDBJ/EMBL/GenBank records are updated
  automatically every 24 hours at all three sites
  now.

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1.2 Primary and Secondary Databases

• The primary databases contain, for the most part,
  experimental results, but are not a curated
  review.
• Curated reviews are found in what are called
  secondary databases.
• The DNA, RNA, or protein sequences are the most
  valuable component of primary databases.

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1.3 Nucleotide Sequence Databases

• The major sources of nucleotide sequence data are
  the databases involved in DDBJ, EMBL, and
  GenBank.
• DDBJ/EMBL/GenBank nucleotide records often are
  the primary source of sequence and biological
  information from which records in other databases
  are derived.

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Database Formats - FASTA
Beginning Symbol
Definition
Accession Number
60 characters per line
Accession Number accession number.version
number Ex. U54469.1
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1.4 Nucleotide Sequence FlatfilesA Dissection

• Flatfiles can be separated into three major
  parts
• Header Apply the information
• (Descriptor) of entire record.
• Feature Table Annotation on the
• record. (Biological information)
• End // on the last line.

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DDBJ/GenBank
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EMBL
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Third Party Annotation (TPA)

• Primary database entries are owned by the
  original submitter and the co-authors of the
  submission publication(s), and owners have
  privileges to update the data contained in the
  record.
• The entries of TPA dataset include reannotations
  of existing entries, combinations of novel
  sequence, and existing primary entries.

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RefSeq (NCBI)

• RefSeq is a curated secondary database that aims
  to provide a comprehensive, integrated,
  nonredundant sets of sequences, including genomic
  DNA, transcripts (RNA), and protein products, for
  selected organisms.

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• NT_123456 Genomic contigs (DNA)
• NM_123456 mRNAs
• NP_123456 Proteins
• XM_123456 Model mRNAs
• XP_123456 Model proteins
• N actual and experimental determined
• X computational prediction

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EMBL Genome Reviews

• The Genome Reviews is a secondary database that
  provides an up-to-date, standardized and
  comprehensively annotated view of the genomic
  sequence of organisms with completely deciphered
  genomes.

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1.5 Protein Sequences Databases

• With the increasing of number of complete genome,
  efforts are now focused on the identification and
  functional analysis of the proteins encoded by
  these genomes.
• Most sequence data in protein databases are
  derived from the translation of nucleotide
  sequences, by and large, they are secondary
  databases.

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• Protein databases can be divided into two broad
  categories
• 1. Sequence repository
• GenPept, UniParc
• 2. Curated database
• RefSeq, UniProt, UniProt knowledgebase

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GenPept - Sequence repository

• Protein sequences in GenPept are derived from
  translations of the sequences in
  DDBJ/EMBL/GenBank and contain the annotation
  present in the nucleotide record.
• GenPept does not contain proteins derived through
  direct amino acid sequencing.
• Redundant database.

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UniParc - Sequence repository

• UniParc contain protein sequences from
  translations of DDBJ/EMBL/GenBank sequences and
  primary protein sequences from direct sequencing
  of proteins.
• Including protein data from Swiss-Prot, TrEMBL,
  PIR-PSD, IPI, RefSeq, FlyBase, and WormBase etc.
• Non-redundant database but No annotation.

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• Non-redundant level
• similar sequences are merged.
• One gene one entry.

Extending annotation and computational analysis
New and update sequences
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UniProt Curated Database
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FTP Sites
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