How to use the web for bioinformatics

1. How to use the web for bioinformatics Molecular Technologies Ethan Strauss ethan.strauss@promega.com 274-4330 X 1171 http://www.q7.com/~ethan

2. Objectives At the end of this session you should be able to do all of the following using freely available tools on the world wide web: Use Genbank or a similar database to find nucleic acid sequences of interest Understand the parts of a Genbank entry Use some of the databases at NCBI to find more information about a sequence. Perform an alignment of several nucleic acid sequences Find an arbitrary tool or database on the web.

3. How to find all those dang URLs! • http://q7.com/~ethan/molbio/

4. Outline • What is Bioinformatics • Sequence Databases • What does a Genbank Entry look like? • Other NCBI databases • Multiple Sequence Alignment • New tools & Databases

5. What is Bioinformatics? • Bioinformatics refers to the creation and advancement of algorithms, computational and statistical techniques, and theory to solve formal and practical problems posed by or inspired from the management and analysis of biological data (Wikipedia)

6. What is Bioinformatics?(my working definition) • Anything done on a computer in which knowledge of biology is helpful. • or • Anything done in biology in which knowledge of computers is helpful.

7. What sort of questions can Bioinformatics answer? • Sequence analysis • Where are restriction sites? • How does an RNA molecule fold? • What changes can be made to a DNA sequence to get a new protein with specific functional changes? • Computational evolutionary biology • How are two sequences related? • Analysis of gene expression • Is this gene highly expressed in cancer cells?

8. What sort of work is done in Bioinformatics? • Measuring biodiversity • How diverse are individuals of a species? • Is it one species or two? • Analysis of regulation • What does this drug do to expression of a gene? • Analysis of mutations in cancer • What is different about these cancer cells as compared to none cancer cells? • High-throughput image analysis • How can we analyze the affects of 1000 different compounds on the location of a specific protein? • And more!

9. Sequence Databases • NCBI databases – Nucleic acids, proteins, Literature, genomes, taxonomy, SNPs and more! • EMBL – Nucleic acid, protein, structure, microarray data and more. • DBJJ – Nucleic acid, protein. • SwissProt – Very well annotated protein database. • Many other general and specialized databases exist.

10. Sequences DatabasesNCBI/Genebank • Nation Center for Biotechnology Information (NCBI) • Sponsored and run by the US government. • Contains many different databases and huge amounts of information. • Most or all data is freely downloadable. • This one site is probably sufficient for all your Nucleic acid and Protein database needs!

11. Sequences DatabasesEntrez • Allows searching and access to NCBI databases.

12. Sequences DatabasesSequence Records • LOCUS Number Size Type Topology Division Date • DEFINITION - Name of the Sequence • ACCESSION - Unique Id number • VERSION - Other numbers which are associated • KEYWORDS • SOURCE – What was it isolated from • ORGANISM - More taxonomic detail • REFERENCE - Paper or papers about the sequence • AUTHORS • TITLE • JOURNAL • FEATURES - A complete list of all of the features of a sequence. Can be very extensive and useful! • ORIGIN – The actual Sequence! • http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=58533118

13. Other NCBI databases • Online Mendelian Inheritance in Man (OMIM) • A catalog of human genes and genetic disorders with links to other NCBI databases, including sequence databases. • This is a good starting point if you want to get sequences for a specific disorder. • http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=omim&term=HFI

14. Other NCBI databases • Gene Database • Gathers information about a single gene. • Exactly one entry per Gene. • A good place to dig deeper into a single gene or to reduce redundancy about a single gene.

15. Other NCBI databases • HomoloGeneGathers homologs from various species • 3D DomainsProtein Structure collection • TaxonomySpecies information • Geo (Gene Expression Omnibus)A gene expression/molecular abundance repository

16. General Utilities • http://searchlauncher.bcm.tmc.edu/seq-util/seq-util.html • Translation • Restriction Digestion • Reformatting (alternately FASTA Formatter) • Complement/Reverse • Etc. • http://www.promega.com/biomath/calc11.htm • Melting Temperature of an oligo.

17. Database search by sequence similarity • Basic Local Alignment Search Tool (BLAST)

18. Multiple Sequence Alignment • Many programs can align multiple sequences with each other to find the best fit for all. • This is generally more biologically meaningful for protein sequences since they are more highly conserved. • Clustal is the most common.

19. Multiple Sequence Alignment • MEAGAYLNAIIFVLVATIIAVISRGLTRTEPCTIRITGESITVHACHIDSX ETIKALA MEAGAYLNAIIFVLVATIIAVISRGLTRTEPCTIRITGESITVHACHIDS...ETIKALA MEA..YLNAII.VLV.TIIAVIS..L.RTEPC.IkITGESITV.ACklDa.....I..L. MEAgaYLNAIIfVLVaTIIAVISrgLtRTEPCtIrITGESITVhAChiDsx etIkaLa • LK PLSLERLFQ LK.PLSLERLFQ ......L..... lk plsLerlfq

20. New Tools • Development of new tools and databases is ongoing. • Your needs will probably change over time. • You can find new tools using • Google • Lists • Nucleic Acids Research Annual Database issue

21. Homework • Assignments due next session • Find a entry of interest in OMIM (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM) • Find a Gene associated with that entry • Click on the “links” link on the right and choose “Gene”

22. Homework • The Gene page has gathered scads of information about this one gene. Find homologs in other species. From this page again choose “links” and go to Homologene

23. Homework • Gather the protein sequences for each homologous gene (or 5 of them if there are more than that). • Click “DownLoad” in the homologene listing • Download everything with the default settings.

24. Homework • You will get a text file in “Fasta” format. Save it somewhere convenient.

25. Homework • Go to the Clustal server at http://searchlauncher.bcm.tmc.edu/multi-align/multi-align.html • Paste your complete Fasta file contents into the input box and click submit. • This takes awhile, so be patient. You will get output that looks something like this.

26. Homework • At the bottom of the alignment file is the same results in “Fasta” format. Copy the complete Fasta results and paste it into the input box at a BoxShade server (http://bioweb.pasteur.fr/seqanal/interfaces/boxshade.html)

27. Homework • Depending on the parameters chosen for BoxShade, you will see something like this. Regions which are the same in all species are likely involved in function in some way.

28. Homework • After all that work, your boss comes to you ands says that sequence comparison is obsolete! He wants you do structural alignments of these proteins. Figure out what a structural alignment is, find two different tools to find conserved 3D structures and choose which one you would use for this. Describe why this tool is preferable to the other. • NOTE: You do not need to actually do any structural alignments. Just find out how you would go about doing on if you had to.