1. Center for Biologisk Sekvensanalyse Nikolaj Blom Center for Biological Sequence Analysis BioCentrum-DTU Technical University of Denmark nikob@cbs.dtu.dk ”Gene Finding in Eukaryotic Genomes” DTU course #27011 30.03.2004

2. Center for Biologisk Sekvensanalyse Today’s plan 13.00-13.40 Get notebooks (building 208; secretary) Lecture on useful tools PFAM, OMIM, UniGene, etc. 13.40-16.00 Work on project Nikolaj present from 13.40-14.00 Lars present from 14.00-14.30

3. Center for Biologisk Sekvensanalyse Practical Stuff WebpageWebpage, Literature, Textbooks Report writing format Contribution from each student specified E.g. Lars & Dorte mainly wrote the Introduction and Methods: Lise & Jens wrote the Results and Discussion sections Repeatmasker http://www.repeatmasker.org/

4. Center for Biologisk Sekvensanalyse Tools For this project you are expected to use only web-based methods. Below is a list of useful links; you are welcome to use some or all of these and to include additional tools. Gene prediction/gene finding programs: GenScan: http://genes.mit.edu/GENSCAN.htmlhttp://genes.mit.edu/GENSCAN.html HMMgene: http://www.cbs.dtu.dk/services/HMMgene/http://www.cbs.dtu.dk/services/HMMgene/ Other tools: RepeatMasker: http://www.repeatmasker.orghttp://www.repeatmasker.org NCBI-BLAST/PSI-BLAST: http://www.ncbi.nlm.nih.gov/BLAST/http://www.ncbi.nlm.nih.gov/BLAST/ PFAM: http://pfam.wustl.edu/http://pfam.wustl.edu/ OMIM: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIMhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM LocusLink http://www.ncbi.nlm.nih.gov/LocusLink/index.htmlhttp://www.ncbi.nlm.nih.gov/LocusLink/index.html UniGene: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene< http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene GeneCardshttp://nciarray.nci.nih.gov/cards/http://nciarray.nci.nih.gov/cards/ InterPro: http://www.ebi.ac.uk/interpro/http://www.ebi.ac.uk/interpro/

5. Center for Biologisk Sekvensanalyse Tools Gene prediction/gene finding programs: *** GenScan: http://genes.mit.edu/GENSCAN.htmlhttp://genes.mit.edu/GENSCAN.html ** HMMgene: http://www.cbs.dtu.dk/services/HMMgene/http://www.cbs.dtu.dk/services/HMMgene/ Other tools: *** RepeatMasker: http://www.repeatmasker.orghttp://www.repeatmasker.org *** NCBI-BLAST/PSI-BLAST: http://www.ncbi.nlm.nih.gov/BLAST/http://www.ncbi.nlm.nih.gov/BLAST/ * PFAM: http://pfam.wustl.edu/http://pfam.wustl.edu/ *** OMIM: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIMhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM ** LocusLink http://www.ncbi.nlm.nih.gov/LocusLink/index.htmlhttp://www.ncbi.nlm.nih.gov/LocusLink/index.html * UniGene: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigenehttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene *** GeneCardshttp://nciarray.nci.nih.gov/cards/http://nciarray.nci.nih.gov/cards/ * InterPro: http://www.ebi.ac.uk/interpro/http://www.ebi.ac.uk/interpro/ *** = very useful for project ** = somewhat useful for project * = less useful for project

6. Center for Biologisk Sekvensanalyse BLAST NCBI-BLAST/PSI-BLAST: http://www.ncbi.nlm.nih.gov/BLAST/ http://www.ncbi.nlm.nih.gov/BLAST/ BLAST=B asic L ocal A lignment S earch T ool Sequence alignment is A powerful way to compare novel sequences with previously characterized genes Homology/similarity may indicate function of novel genes/proteins

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11. PFAM PFAM: http://pfam.wustl.edu/http://pfam.wustl.edu/ The Pfam database of protein families and HMMs Analyze your sequence for matches to known protein families

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15. OMIM – Online Mendelian Inheritance in Man OMIM http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?d b=OMIMhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?d b=OMIM Human curators Gene function, Effect in animal models References Fantastic resource!

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19. LocusLink http://www.ncbi.nlm.nih.gov/LocusLink/index.ht mlhttp://www.ncbi.nlm.nih.gov/LocusLink/index.ht ml Single query interface to curated sequence and descriptive information about genetic loci Nomenclature, aliases, sequence accessions, phenotypes, EC numbers, MIM numbers, UniGene clusters, homology, map locations, and related web sites

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22. UniGene UniGene: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?d b=unigenehttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?d b=unigene Experimental system for automatically partitioning GenBank sequences into a non-redundant set of gene-oriented clusters Each UniGene cluster contains sequences that represent a unique gene Expression information Tissue types in which the gene has been expressed and map location

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24. GeneCards http://nciarray.nci.nih.gov/cards/ GeneCards™ is a database of human genes, their products and their involvement in diseases. It offers concise information about the functions of all human genes that have an approved symbol, as well as selected others Excellent gene overview!

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27. InterPro InterPro: http://www.ebi.ac.uk/interpro/ InterPro is an integrated documentation resource for protein families, domains and sites. InterPro combines a number of databases (referred to as member databases) that use different methodologies and a varying degree of biological information on well-characterised proteins to derive protein signatures. By uniting the member databases, InterPro capitalises on their individual strengths, producing a powerful integrated diagnostic tool

28. Center for Biologisk Sekvensanalyse InterPro InterPro: Advanced Not so easy to use Includes e.g. PFAM + other resources

29. Center for Biologisk Sekvensanalyse Tools Gene prediction/gene finding programs: *** GenScan: http://genes.mit.edu/GENSCAN.htmlhttp://genes.mit.edu/GENSCAN.html ** HMMgene: http://www.cbs.dtu.dk/services/HMMgene/http://www.cbs.dtu.dk/services/HMMgene/ Other tools: *** RepeatMasker: http://www.repeatmasker.orghttp://www.repeatmasker.org *** NCBI-BLAST/PSI-BLAST: http://www.ncbi.nlm.nih.gov/BLAST/http://www.ncbi.nlm.nih.gov/BLAST/ * PFAM: http://pfam.wustl.edu/http://pfam.wustl.edu/ *** OMIM: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIMhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM ** LocusLink http://www.ncbi.nlm.nih.gov/LocusLink/index.htmlhttp://www.ncbi.nlm.nih.gov/LocusLink/index.html * UniGene: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene<http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene *** GeneCardshttp://nciarray.nci.nih.gov/cards/http://nciarray.nci.nih.gov/cards/ * InterPro: http://www.ebi.ac.uk/interpro/http://www.ebi.ac.uk/interpro/ *** = very useful for project ** = somewhat useful for project * = less useful for project

30. Center for Biologisk Sekvensanalyse The End