National Center for Biotechnology
Information (NCBI)
www.ncbi.nlm.nih.gov
   
   
Entrez is a search and retrieval system 
that integrates NCBI databases
   
BLAST is...
ˇ Basic Local Alignment Search Tool
ˇ NCBI's sequence similarity search tool
ˇ supports analysis of DNA and protein databases
ˇ 80,000 searches per day
   
OMIM is...
ˇOnline Mendelian Inheritance in Man
čatalog of human genes and genetic disorders
ědited by Dr. Victor McKusick, others at JHU
   
   
What is an accession number?
An accession number is label that used to identify a sequence. It is a 
string of letters and/or numbers that corresponds to a molecular 
sequence. 
Examples (all for retinol­binding protein, RBP4):
X02775 GenBank genomic DNA sequence
NT_030059 Genomic contig
Rs7079946 dbSNP (single nucleotide polymorphism)
N91759.1 An expressed sequence tag (1 of 170)
NM_006744 RefSeq DNA sequence (from a transcript)
NP_007635 RefSeq protein
AAC02945 GenBank protein
Q28369 SwissProt protein
1KT7 Protein Data Bank structure record
protein
DNA
RNA
   
   
   
   
FASTA format
   
Graphical format
   
European Molecular Biology Laboratory
European Bioinformatics Institute
 (EMBL­EBI)
http://www.ebi.ac.uk/
   
   
   
Uniprot
http://www.ebi.uniprot.org
   
   
Interpro
http://www.ebi.ac.uk/interpro
   
   
Swiss Institute of Bioinformatics
(SIB)
http://www.isb­sib.ch
   
   
   
UCSC Genome Browser
(GB)
http://genome.ucsc.edu
   
   
Biology Workbench
http://workbench.sdsc.edu
   
   
Protein Data Bank
(PDB)
http://www.pdb.org
   
Sequenced genomes ENSEMBL ~200
DNA sequences NCBI 30 000 000
PROTEIN sequences UniProtKB 4 134 341
PROTEIN structures PDB 42212
   
Praktické cvičení
 Vyhledejte DNA i proteinovou sekvenci
lidského rhodopsinu
 NCBI Entrez http://www.ncbi.nlm.nih.gov/
 Vyhledejte 3-D strukturu rhodopsinu s
organizmu nejbližšího člov kuě
 http://pdbbeta.rcsb.org/pdb/
 Srovnejte proteinové sekvence obou proteinů
 http://clustalw.genome.jp/
   
Rhodopsin
 NT_005612 (contig, 35742636-35749341)
 NC_000003 (chr03, 130730180-130736885, map
3q21-q24)
 NM_000539 (mRNA)
 NP_000530 (protein RHO, RP4, OPN2)
 PDB bovine RHO: 1F88 1GZM 1HZX 1JFP 1L9H 1U19
1LN6
 23 mismatches in sequence alignment