1. Lesson 3 Bioinformatics Laboratory
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Lesson 3
Bioinformatics Laboratory
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2. EMBnet European Molecular Biology Network
In 1988 a network was established to link European laboratories that used bio-computing and bioinformatics in molecular biology research.
In each country a national node provides local bio-computing services
INN serves as Israel’s National Node
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3. Israel National Node INN serves as Israel’s National Node
Authorized by the Ministry of Science in 1990.
INN is located at the Biological Computing Unit, Weizmann Institute of Science.
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4. Bioinformatics Units at Universities
In Israel, in the mid 1990s Bioinformatics Units arose at Universities to serve local needs
At TAU –
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5. Database Interrogation
Two ways to search databases
Database interrogation – searches textual information contained in header sections of database entries
Database searching – searches sequence information with sequence queries
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6. Database Interrogation Problem of EMBnet
No effective way of interrogating all the resources together at a particular site, since formats differ
A research project was undertaken with EMBnet to address problems inherent in interfacing complex environments – resulting in SRS – sequence retrieval system, a network browser for databases in molecular biology
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7. SRS SRS allows any flat file database to be indexed to any other.
Powerful tool that allows users to formulate queries across a range of different database types via a single interface, without having to worry about underlying data structures, query languages, etc.
Sequence
Retrieval
System
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8. SRS – List of Public SRS Servers
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9. SRS – List of Public SRS Servers
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10. Searching SRS
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11. SRS Tutorial
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12. Search SRS Databases
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13. SRS Standard Query Form
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14. SRS Standard Query Form
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15. SRS Extended Query Form
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16. NCBI National Center for Biotechnology
Established in 1988 and located at the campus of NIH as a subdivision of NLM (National Library of Medicine)
Since 1992 one of NCBI’s major tasks has been maintenance of GenBank
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17. Entrez
Entrez allows retrieval of molecular biology data and bibliographic citations from NCBI’s integrated databases
Entrez, unlike SRS, does not allow customization with an institute’s preferred databases
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18. Entrez
Most records are linked to other records, within a given database and between databases
Sequence databases are linked to the Medline databases so that one can move from paper to sequence and vice versa seamlessly
“Neighboring” allows related papers in Medline, with similar subjects, and sequence entries, found through blast searches, to be grouped together
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19. Entrez at NCBI
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Web Servers

20. Entrez at NCBI
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21. Entrez at NCBI
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22. Entrez Pros and Cons Pros Cons
Integrates reference database with sequence database seamlessly
Cons
Very dependent on the network link as databases being searched are in the US
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23. GCG Software Package Similar syntax to Unix commands
Write GCG in every new window to start the program
Same principles for all programs:
Write command and arguments
Choose Parameters (default parameters)
Receive an output (screen and file)
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24. Searching with GCG
Stringsearch: a simple text-search through local databases.
Searching through definitions or through full annotations.
The definitions contain a minimal amount of the information for each entry: accession, organism name, gene name, sequence length, date.
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25. Searching with GCG Annotations take much longer to search through
The annotations contain the complete documentation for each entry in the sequence database, including journal and author names, sequence features, comments, etc.
Annotations take much longer to search through
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26. Getting a sequence
Fetch: Get a sequence file to your account using the accession number or the id code. Example: fetch hum_hbb
Fetches all the files with the given accession number. Can be limited to a certain data base using database code:
Example: fetch embl:u01613
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27. Sequence formats Different applications use different sequence format.
GCG
FASTA/Pearson
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28. Changing file formats
Two GCG commands are used to convert file format.
tofasta
formfasta
Similar commands (fromembl, topir etc)
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