Information networks
Bioinformatics - lectures
Introduction Information networks Protein information resources Genome information resources DNA sequence analysis Pairwise sequence alignment Multiple sequence alignment Secondary database searching Analysis packages Protein structure modelling
Information networks
what is the Internet?
how do computers find each other? FTP and Telnet what is the Worl Wide Web? HTTP, HTML and URL
EMBnet, EBI, NCBI SRS and ENTREZ
What is the Internet?
Global network of computer networks that link government, academic and business institutions.
communication by TCP/IP
(Transmission Control Protocol/Internet Protocol)
computers - nodes, data - packets
packets may not be transferred directly from one computer to another
How do computers find each other?
Each computer is assigned IP address
147.251.28.2
machine.site.domain bilbo.chemi.muni.cz
FTP - File Transfer Protocol
Telnet - remote connection
Example of Internet domains and subdomains
Country-based domains		Other domains		Subdomains
Australia	.au	Educational	,edu	Academic
Denmark	.dk	Commercial	.com	Company
Finland	.fi	Governmental	.gov	Other organisation
France	.fr	Military	.mil	General
Germany	.de			
Greece	-gr			
Hungary	.hu			
Ireland	.ie			
Israel	.iL			
Italy	.it			
Netherlands	.nl			
New Zealand	.nz			
Poland	.pi			
Portugal	.pt			
South Africa	.za			
Spain	.es			
Sweden	-se			
Switzerland	.ch			
United Kingdom	.uk			
USA	.us			
What is the World Wide Web?
■  Developed at CERN - the European Laboratory of Particle Physics.
■ The purpose was sharing of information
Hypermedia based information system.
The most advanced information system found on the web.
Very popular - almost synonymous with the Internet.
Web browsers
■ Browser is the client communicating with servers using standard protocols.
Home page is the first point of contact between browser and the server.
Lynx - academic, VT100 terminal
Mosaic - academic, X-windows
Netscape Navigator - commercial Internet Explorer - commercial
HTTP, HTML and URL
■ HTTP - HyperText Transport Protocol
documents exploited by browsers are written in hypertext and transferred by HTTP
HTML - HyperText markup Language standard language for writing a hypertext
URL - Uniform Resourse Locator unique address for a document example: http://www.chemi.muni.cz/~jiri
EMBnet, EBI, NCBI
1988 established the network of European biocomputing and bioinformatics laboratories.
Eliminates the need for multicopies of biology databases and retrieval software.
Hinxton Hall = Sanger Centre + MRC Human Genome Mapping Project Resource Centre +
European Bioinformatics Institute (EBI)
National Center for Biotechnology Information (NCBI)
SRS, ENTREZ and LinkDB
SRS - The Sequence Retrieval System
** maintained by EBI
** network browser for databases in molecular biology
** allows indexation of flat-file databases
** allows customised search of selected databases
»link databanks: sequence, structure, bibliography, etc
ENTREZ
** integrates databases of NCBI
** less flexible then SRS
** valuable concept of neighbouring
** link databanks: DNA and protein sequences, genome data, structural data, PubMed bibliography
SRS, ENTREZ and LinkDB
LinkDB
maintained by Institute for Chemical Reseach, Japan
network browser for databases in DBGET and KEGG (Kyoto encyclopedia of genes and genomes)
link databanks: sequence, motifs, structure, amino acid properties, ligands, metabolic pathways
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Protein Sequences
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DBGET Database Links
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