Introduction to other web based resources
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Introduction to other web-based resources. What? Where? and How? of Bioinformatics June 3, 2009. Protein seq. DNA seq. Protein structure. Protein function. Applications. Bioinformatics.

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Introduction to other web based resources

Introduction to other web-based resources

What? Where? and How? of Bioinformatics

June 3, 2009


Bioinformatics

Protein seq

DNA seq

Protein

structure

Protein function

Applications

Bioinformatics

“Bioinformatics is the application of computer technology to the management and analysis of biological data. The result is that computers are being used to gather, store, analyse and merge biological data.”

(http://www.ebi.ac.uk/2can/bioinformatics/bioinf_what_1.html)


Real life bioinformatics

Real-life Bioinformatics

  • Primary Data

    • Gene or protein sequence

      • GenBank/EMBL/DDBJ, UniProt

    • Protein structure

      • wwPDB

    • Gene or protein interactions

      • IntAct, DIP, BioGRID

    • Functional studies

      • PubMed

      • Specialized databases (enzymes >> kinases)

  • Secondary Data

    • Protein families

      • Pfam, Interpro

    • Protein structure classifications

      • SCOP, CATH

    • Protein location, function

      • GO


Where do we start

Gene name &

synonyms

Micro-array

Data

Gene

expression

Disease/

SNP

Gene

sequence

Protein

interactions

Protein

sequence

Protein

structure

Protein name &

synonyms

Protein

domains

Protein

function

Where do we start?


Rcsb links

RCSB links


Ncbi links

NCBI links

http://www.ncbi.nlm.nih.gov/Sitemap/index.html


Ncbi bioinformatics tutorials

NCBI bioinformatics tutorials

http://www.ncbi.nlm.nih.gov/Education/index.html


Ebi links

EBI links

http://www.ebi.ac.uk/


Kegg links

KEGG links

http://www.genome.jp/kegg/kegg2.html


Should i believe all i read find

Should I believe all I read/find?

  • Source of information? (where/who)

    • Scientific article?

    • Web-based resource?

    • Text book or other?

  • Evidence for the conclusion? (how)

    • Scientific experiment

    • Electronic annotation

    • Based on homology

      • Sequence

      • Modeling

    • Hypothesis/generalization


How to read a scientific paper

How to read a scientific paper

  • Read Abstract

  • Read Introduction

  • Read Conclusion / Discussion

  • Read Methods

  • Review figures and figure legend

    • Draw your own conclusion based on data presented

    • Do you agree with the author’s conclusion?

  • Read results details


Searching for lysozyme

Searching for Lysozyme

  • My name is Lysozyme. How well do you know me?

Independently find all that you can about Lysozyme and make a report.


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