04_Databases

By Yan Li

PhD in Bioinformatics, University of Liverpool

Major databases

  • DNA sequence databases
    • NCBI (US GenBank)
    • EBI (European EMBL-Bank)
    • DDBJ (Asia)
  • Protein sequence database
    • UniProtKB (incorporates Swiss-Prot)
  • Protein structure database
    • PDB
  • Pathway database
    • KEGG
    • GO

Specialised databases

specialised databases

Boolean operators

  • AND, OR and NOT
  • Must be capitalised
  • Operators are processed left to right
  • e.g.: globin AND promoter OR enhancer

Boolean operators

Boolean operators

fasta file

  • A header line: >ID description
  • Use IUPAC standard one-letter code, nucleotides or amino acides
  • Format extension: fasta, fa, fna, faa, etc.
>sp|P02700|OPSD_SHEEP Rhodopsin - Ovis aries (Sheep) 
MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY 
VTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLG 
GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIP 
QGMQCSCGALYFTLKPEINNESFVIYMFVVHFSIPLIVIFFCYGQLVFTVKEAAAQQQES 
ATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKSSSV 
YNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTVSKTETSQVAPA

GFF file

  • \t separated table of genome annotation
#seqid  source  type    start   end score   strand  phase   attributes
CP255_v1_chr	Bacpipe	CDS	169	255	.	+	.	ID=CP255_00001;gene_biotype=protein_coding;Name=thrL;note=blasn name thrL;
CP255_v1_chr	Bacpipe	CDS	337	2799	.	+	.	ID=CP255_00002;gene_biotype=protein_coding;Name=thrA;Dbxref=WP_001264677.1;note=bifunctional aspartate kinase/homoserine dehydrogenase I;
CP255_v1_chr	Bacpipe	CDS	2801	3730	.	+	.	ID=CP255_00003;gene_biotype=protein_coding;Name=thrB;Dbxref=WP_000241685.1;note=homoserine kinase;
CP255_v1_chr	Bacpipe	CDS	3734	5020	.	+	.	ID=CP255_00004;gene_biotype=protein_coding;Name=thrC;Dbxref=WP_000781109.1;note=threonine synthase;

genbank file

  • An annotation (and sequence) file format used by NCBI, gene bink,
  • First 10 characters form a column of identifier,
  • Followed by infomations

Visualizing genome

Artemis

Artemis

Workshop