Practical Bioinformatics Chapter 1: Introduction to Bioinformatics

Introduction to Practical Bioinformatics Databases and Basic Queries 1 Practical Bioinformatics is taught at http://bioinf.moodlehub.com Goals  In this chapter you will learn about the various tools available on the NCBI website and how to find scientific papers using PubMed. At the end you should be able to do the following.  Navigate the NCBI website  Use the Entrez browser to query PubMed and GenBank 2 Practical Bioinformatics is taught at http://bioinf.moodlehub.com Practical Bioinformatics Online  A 5 week course with live, prerecorded and self-taught learning exercises  Teaches how to use powerful and free tools and databases. Does not include math or computer programming concepts.  Designed for advanced high school, undergraduate and graduate students  Also appropriate for biotech patent law and medical professionals  Students enroll before taking the class  http://bioinf.moodlehub.com Practical Bioinformatics is taught at http://bioinf.moodlehub.com 3 Bioinformatics  Definitions  A collection of tools used to study DNA and protein sequences and biological relationships  The interface between a human brain and a sequence database  A sub-discipline of computational biology  Bioinformatics tools let you research and discover genes, gene regulator regions and proteins in free databases. 4 Practical Bioinformatics is taught at http://bioinf.moodlehub.com Purpose of Bioinformatics  DNA and protein sequence data is accumulating in vast database repositories as a result of genome sequencing projects and individual molecular biology research  The data consists of long text string, often with little formatting or annotation.  Humans need specialized computer tools to access and understand this data 5 Practical Bioinformatics is taught at http://bioinf.moodlehub.com CACCTAAATTGTAAGCGTTAATATTTTGTTAAAATTCGCGTTAAATTTTTGTTAAATCAGCTCATTTTTTGCTCGGCTCGCATCGCAGATACTACGACGAGCACGAC AACCAATAGGCCGAAATCGGCAAAATCCCTTATAAATCAAAAGAATAGACCGAGATAGGGTTGAGTGTTGGATTAATCGATCGACAAGCTCACGAGATGTACGC TTCCAGTTTGGAACAAGAGTCCACTATTAAAGAACGTGGACTCCAACGTCAAAGGGCGAAAAACCGTCTAGATGATAGCGCATCATCGACATCGAATTCGATGAC TCAGGGCGATGGCCCACTACGTGAACCATCACCCTAATCAAGTTTTTTGGGGTCGAGGTGCCGTAAAGCAGAGTCAATCACGATCATTAGCTGGCGCGTACATCG CTAAATCGGAACCCTAAAGGGAGCCCCCGATTTAGAGCTTGACGGGGAAAGCCGGCGAACGTGGCGAGAAGTATTACGCGGCGCAGATCGACGAGCACAGACCG AGGAAGGGAAGAAAGCGAAAGGAGCGGGCGCTAGGGCGCTGGCAAGTGTAGCGGTCACGCTGCGCGTAACGATGACTGCGGCGATATATCGACGATCGACGAC CACCACACCCGCCGCGCTTAATGCGCCGCTACAGGGCGCGTCCCATTCGCCATTCAGGCTGCGCAACTGTGTATTAGCGGATCGATCGACGACGACAGCGGCGCG TGGGAAGGGCGATCGGTGCGGGCCTCTTCGCTATTACGCCAGCTGGCGAAAGGGGGATGTGCTGCAAGGCTATGAGCGCGGCGATATGCGACTGACTCGCGCGC GATTAAGTTGGGTAACGCCAGGGTTTTCCCAGTCACGACGTTGTAAAACGACGGCCAGTGAATTGTAATAGATATGCTACGCATCGACGATCGATGCGCTAATGA CGACTCACTATAGGGCGAATTGGGTACCGGGCCCCCCCTCGAGGTCGACGGTATCGATAAGCTTGATATCGAGTTAGCGACTACGATCGATGTTAGTAGCAGCCC GAATTCCTGCAGCCCGGGGGATCCACTAGTTCTAGAGCGGCCGCCACCGCGGTGGAGCTCCAGCTTTTGTGATGACTAGCAGCATGCTAGCAGCAATCGGCGCG TCCCTTTAGTGAGGGTTAATTTCGAGCTTGGCGTAATCATGGTCATAGCTGTTTCCTGTGTGAAATTGTTGATCGATGCTAGATGCGACTGACGATCGATCGACAA ATCCGCTCACAATTCCACACAACATACGAGCCGGAAGCATAAAGTGTAAAGCCTGGGGTGCCTAATGAGTGATGCATCGATGCTACGTAGCTAGACAGCTAGCTA GAGCTAACTCACATTAATTGCGTTGCGCTCACTGCCCGCTTTCCAGTCGGGAAACCTGTCGTGCCAGCTGGTACGTAGCTACGTAGCTACGATCGATGCATACGCC CATTAATGAATCGGCCAACGCGCGGGGAGAGGCGGTTTGCGTATTGGGCGCTCTTCCGCTTCCTCGCTCAGATGCTACGATGCTAGCTAGTAGCTGACGATCGTCG CTGACTCGCTGCGCTCGGTCGTTCGGCTGCGGCGAGCGGTATCAGCTCACTCAAAGGCGGTAATACGGTTGATCTGAGCGACGTATCAGTGATGCAGCTGCGATG ATCCACAGAATCAGGGGATAACGCAGGAAAGAACATGTGAGCAAAAGGCCAGCAAAAGGCCAGGAACCGTGTAGCTAGTAGCTAGCTAGTGATATATTGCGCG AAAAAGGCCGCGTTGCTGGCGTTTTTCCATAGGCTCCGCCCCCCTGACGAGCATCACAAAAATCGACGCTGCAGATTATTATGCTGATCGATCGATCGACGTGCTG CAAGTCAGAGGTGGCGAAACCCGACAGGACTATAAAGATACCAGGCGTTTCCCCCTGGAAGCTCCCTCGTGATCTAGCTACGATCGACTGATATATATATATGCG GCGCTCTCCTGTTCCGACCCTGCCGCTTACCGGATACCTGTCCGCCTTTCTCCCTTCGGGAAGCGTGGCGGATGCTAGCTAGCTAGCTAGTGCTGATCGAZTCGTAG CTTTCTCATAGCTCACGCTGTAGGTATCTCAGTTCGGTGTAGGTCGTTCGCTCCAAGCTGGGCTGTGTGCGATGTAGCTAGCTGTGATCGFCGATGCTGCTGTAGAG ACGAACCCCCCGTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGTAAGGATCGTAGTCGTAGTAGCTAGTACGTAGATGCCGCG ACACGACTTATCGCCACTGGCAGCAGCCACTGGTAACAGGATTAGCAGAGCGAGGTATGTAGGCGGTGCTGTAGCTAGCATGATCGATGTAGCTGCGCGCGCGCC ACAGAGTTCTTGAAGTGGTGGCCTAACTACGGCTACACTAGAAGGACAGTATTTGGTATCTGCGCTCTGCATCGACTAGCTAGCTAGCATCGTACGTACGTAGTGG TGAAGCCAGTTACCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAACCACCGCTGGTAGCGGGATCGATCGTACGTAGCTAGCTACGTAGCTAGCTG TGGTTTTTTTGTTTGCAAGCAGCAGATTACGCGCAGAAAAAAAGGATCTCAAGAAGATCCTTTGATCTTTGATGCATGCTAGCACTGATCGATCGTAGCTACGTGC TCTACGGGGTCTGACGCTCAGTGGAACGAAAACTCACGTTAAGGGATTTTGGTCATGAGATTATCAAAAATACGTAGCTAGTATTCGCGCTAGCTACGGATCGTG GGATCTTCACCTAGATCCTTTTAAATTAAAAATGAAGTTTTAAATCAATCTAAAGTATATATGAGTAAACGATGCTAGTAGCTGATCAGTAGCTGCTGATAGTGC TTGGTCTGACAGTTACCAATGCTTAATCAGTGAGGCACCTATCTCAGCGATCTGTCTATTTCGTTCATCCGTAACGCGCGTATACGATCATCTACTCAGCGCTGGG ATAGTTGCCTGACTCCCCGTCGTGTAGATAACTACGATACGGGAGGGCTTACCATCTGGCCCCAGTGCTGGATGCTAGTACTATGCGGCGCGCTATGATCATGTC CAATGATACCGFOURSCOREANDSEVENYEARSAGOGATTTATCAGCAATAAACCAGCCAGCCGGAAGGGCGTAGTAGCTAGTATACGTCAGTAGTGACTCGTG CGAGCGCAGAAGTGGTCCTGCAACTTTATCCGCCTCCATCCAGTCTATTAATTGTTGCCGGGAAGCTAGAAGATCATGCTAGCGTACGACTAGCTAGCTGCTGGG GTAAGTAGTTCGCCAGTTAATAGTTTGCGCAACGTTGTTGCCATTGCTACAGGCATCGTGGTGTCACGCTGATGCTACGGCTAGTCGATGCTGATACGCTAGCATA CGTCGTTTGGTATGGCTTCATTCAGCTCCGGTTCCCAACGATCAAGGCGAGTTACATGATCCCCCATGTTGCTAGCTACACGACCGCGGCGATCTCAGATAGCGCG GTGCAAAAAAGCGGTTAGCTCCTTCGGTCCTCCGATCGTTGTCAGAAGTAAGTTGGCCGCAGTGTTATCAGATGATGCATCGATCGATGCATCGATGTAGTGCTCG CTCATGGTTATGGCAGCACTGCATAATTCTCTTACTGTCATGCCATCCGTAAGATGCTTTTCTGTGACTGGACTAGCTACGTAGCTAGCATAGCTAGCTGACGATGG GTGAGTACTCAACCAAGTCATTCTGAGAATAGTGTATGCGGCGACCGAGTTGCTCTTGCCCGGCGTCAATGATCGTAGCTAGACTGTGGAGTACTATGCGCGCGG ACGGGATAATACCGCGCCACATAGCAGAACTTTAAAAGTGCTCATCATTGGAAAACGTTCTTCGGGGCGAGATCGTAGCTACGACGTCGCGGCTATATTGCGAGT AAACTCTCAAGGATCTTACCGCTGTTGAGATCCAGTTCGATGTAACCCACTCGTGCACCCAACTGATCTTGATGCTAGTCGATCGATCGTACGTATACGCGCTAGC CAGCATCTTTTACTTTCACCAGCGTTTCTGGGTGAGCAAAAACAGGAAGGCAAAATGCCGCAAAAAAGGGGTAGCTAGCTAGCTGTAGATCGCGATGCGCGGCGA AATAAGGGCGACACGGAAATGTTGAATACTCATACTCTTCCTTTTTCAATATTATTGAAGCATTTATCAGGATCGTACTATCGCGGCGCGCGATCGCGGACTCTAC GGTTATTGTCTCATGAGCGGATACATATTTGAATGTATTTAGAAAAATAAACAAATAGGGGTTCCGCGCAGATGCATGCTAGCAGCATCGATCGTACGATGACGG CATTTCCCCGAAAAGTGCGATACTGACGCTACGATGCTACTACTGACGTCGTACCGCGATATATGCGCGTATCGCAGTACTACGCGCGCGATCGCATGACTGTGGG 6 An bioinformatics analogy CACCTAAATTGTAAGCGTTAATATTTTGTTAAAATTCGCGTTAAATTTTTGTTAAATCAGCTCATTTTTTGCTCGGCTCGCATCGCAGATACTACGACGAGCACGAC AACCAATAGGCCGAAATCGGCAAAATCCCTTATAAATCAAAAGAATAGACCGAGATAGGGTTGAGTGTTGGATTAATCGATCGACAAGCTCACGAGATGTACGC TTCCAGTTTGGAACAAGAGTCCACTATTAAAGAACGTGGACTCCAACGTCAAAGGGCGAAAAACCGTCTAGATGATAGCGCATCATCGACATCGAATTCGATGAC TCAGGGCGATGGCCCACTACGTGAACCATCACCCTAATCAAGTTTTTTGGGGTCGAGGTGCCGTAAAGCAGAGTCAATCACGATCATTAGCTGGCGCGTACATCG CTAAATCGGAACCCTAAAGGGAGCCCCCGATTTAGAGCTTGACGGGGAAAGCCGGCGAACGTGGCGAGAAGTATTACGCGGCGCAGATCGACGAGCACAGACCG AGGAAGGGAAGAAAGCGAAAGGAGCGGGCGCTAGGGCGCTGGCAAGTGTAGCGGTCACGCTGCGCGTAACGATGACTGCGGCGATATATCGACGATCGACGAC CACCACACCCGCCGCGCTTAATGCGCCGCTACAGGGCGCGTCCCATTCGCCATTCAGGCTGCGCAACTGTGTATTAGCGGATCGATCGACGACGACAGCGGCGCG TGGGAAGGGCGATCGGTGCGGGCCTCTTCGCTATTACGCCAGCTGGCGAAAGGGGGATGTGCTGCAAGGCTATGAGCGCGGCGATATGCGACTGACTCGCGCGC GATTAAGTTGGGTAACGCCAGGGTTTTCCCAGTCACGACGTTGTAAAACGACGGCCAGTGAATTGTAATAGATATGCTACGCATCGACGATCGATGCGCTAATGA CGACTCACTATAGGGCGAATTGGGTACCGGGCCCCCCCTCGAGGTCGACGGTATCGATAAGCTTGATATCGAGTTAGCGACTACGATCGATGTTAGTAGCAGCCC GAATTCCTGCAGCCCGGGGGATCCACTAGTTCTAGAGCGGCCGCCACCGCGGTGGAGCTCCAGCTTTTGTGATGACTAGCAGCATGCTAGCAGCAATCGGCGCG TCCCTTTAGTGAGGGTTAATTTCGAGCTTGGCGTAATCATGGTCATAGCTGTTTCCTGTGTGAAATTGTTGATCGATGCTAGATGCGACTGACGATCGATCGACAA ATCCGCTCACAATTCCACACAACATACGAGCCGGAAGCATAAAGTGTAAAGCCTGGGGTGCCTAATGAGTGATGCATCGATGCTACGTAGCTAGACAGCTAGCTA GAGCTAACTCACATTAATTGCGTTGCGCTCACTGCCCGCTTTCCAGTCGGGAAACCTGTCGTGCCAGCTGGTACGTAGCTACGTAGCTACGATCGATGCATACGCC CATTAATGAATCGGCCAACGCGCGGGGAGAGGCGGTTTGCGTATTGGGCGCTCTTCCGCTTCCTCGCTCAGATGCTACGATGCTAGCTAGTAGCTGACGATCGTCG CTGACTCGCTGCGCTCGGTCGTTCGGCTGCGGCGAGCGGTATCAGCTCACTCAAAGGCGGTAATACGGTTGATCTGAGCGACGTATCAGTGATGCAGCTGCGATG ATCCACAGAATCAGGGGATAACGCAGGAAAGAACATGTGAGCAAAAGGCCAGCAAAAGGCCAGGAACCGTGTAGCTAGTAGCTAGCTAGTGATATATTGCGCG AAAAAGGCCGCGTTGCTGGCGTTTTTCCATAGGCTCCGCCCCCCTGACGAGCATCACAAAAATCGACGCTGCAGATTATTATGCTGATCGATCGATCGACGTGCTG CAAGTCAGAGGTGGCGAAACCCGACAGGACTATAAAGATACCAGGCGTTTCCCCCTGGAAGCTCCCTCGTGATCTAGCTACGATCGACTGATATATATATATGCG GCGCTCTCCTGTTCCGACCCTGCCGCTTACCGGATACCTGTCCGCCTTTCTCCCTTCGGGAAGCGTGGCGGATGCTAGCTAGCTAGCTAGTGCTGATCGAZTCGTAG CTTTCTCATAGCTCACGCTGTAGGTATCTCAGTTCGGTGTAGGTCGTTCGCTCCAAGCTGGGCTGTGTGCGATGTAGCTAGCTGTGATCGFCGATGCTGCTGTAGAG ACGAACCCCCCGTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGTAAGGATCGTAGTCGTAGTAGCTAGTACGTAGATGCCGCG ACACGACTTATCGCCACTGGCAGCAGCCACTGGTAACAGGATTAGCAGAGCGAGGTATGTAGGCGGTGCTGTAGCTAGCATGATCGATGTAGCTGCGCGCGCGCC ACAGAGTTCTTGAAGTGGTGGCCTAACTACGGCTACACTAGAAGGACAGTATTTGGTATCTGCGCTCTGCATCGACTAGCTAGCTAGCATCGTACGTACGTAGTGG TGAAGCCAGTTACCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAACCACCGCTGGTAGCGGGATCGATCGTACGTAGCTAGCTACGTAGCTAGCTG TGGTTTTTTTGTTTGCAAGCAGCAGATTACGCGCAGAAAAAAAGGATCTCAAGAAGATCCTTTGATCTTTGATGCATGCTAGCACTGATCGATCGTAGCTACGTGC TCTACGGGGTCTGACGCTCAGTGGAACGAAAACTCACGTTAAGGGATTTTGGTCATGAGATTATCAAAAATACGTAGCTAGTATTCGCGCTAGCTACGGATCGTG GGATCTTCACCTAGATCCTTTTAAATTAAAAATGAAGTTTTAAATCAATCTAAAGTATATATGAGTAAACGATGCTAGTAGCTGATCAGTAGCTGCTGATAGTGC TTGGTCTGACAGTTACCAATGCTTAATCAGTGAGGCACCTATCTCAGCGATCTGTCTATTTCGTTCATCCGTAACGCGCGTATACGATCATCTACTCAGCGCTGGG ATAGTTGCCTGACTCCCCGTCGTGTAGATAACTACGATACGGGAGGGCTTACCATCTGGCCCCAGTGCTGGATGCTAGTACTATGCGGCGCGCTATGATCATGTC CAATGATACCGFOURSCOREANDSEVENYEARSAGOGATTTATCAGCAATAAACCAGCCAGCCGGAAGGGCGTAGTAGCTAGTATACGTCAGTAGTGACTCGTG CGAGCGCAGAAGTGGTCCTGCAACTTTATCCGCCTCCATCCAGTCTATTAATTGTTGCCGGGAAGCTAGAAGATCATGCTAGCGTACGACTAGCTAGCTGCTGGG GTAAGTAGTTCGCCAGTTAATAGTTTGCGCAACGTTGTTGCCATTGCTACAGGCATCGTGGTGTCACGCTGATGCTACGGCTAGTCGATGCTGATACGCTAGCATA CGTCGTTTGGTATGGCTTCATTCAGCTCCGGTTCCCAACGATCAAGGCGAGTTACATGATCCCCCATGTTGCTAGCTACACGACCGCGGCGATCTCAGATAGCGCG GTGCAAAAAAGCGGTTAGCTCCTTCGGTCCTCCGATCGTTGTCAGAAGTAAGTTGGCCGCAGTGTTATCAGATGATGCATCGATCGATGCATCGATGTAGTGCTCG CTCATGGTTATGGCAGCACTGCATAATTCTCTTACTGTCATGCCATCCGTAAGATGCTTTTCTGTGACTGGACTAGCTACGTAGCTAGCATAGCTAGCTGACGATGG GTGAGTACTCAACCAAGTCATTCTGAGAATAGTGTATGCGGCGACCGAGTTGCTCTTGCCCGGCGTCAATGATCGTAGCTAGACTGTGGAGTACTATGCGCGCGG ACGGGATAATACCGCGCCACATAGCAGAACTTTAAAAGTGCTCATCATTGGAAAACGTTCTTCGGGGCGAGATCGTAGCTACGACGTCGCGGCTATATTGCGAGT AAACTCTCAAGGATCTTACCGCTGTTGAGATCCAGTTCGATGTAACCCACTCGTGCACCCAACTGATCTTGATGCTAGTCGATCGATCGTACGTATACGCGCTAGC CAGCATCTTTTACTTTCACCAGCGTTTCTGGGTGAGCAAAAACAGGAAGGCAAAATGCCGCAAAAAAGGGGTAGCTAGCTAGCTGTAGATCGCGATGCGCGGCGA AATAAGGGCGACACGGAAATGTTGAATACTCATACTCTTCCTTTTTCAATATTATTGAAGCATTTATCAGGATCGTACTATCGCGGCGCGCGATCGCGGACTCTAC GGTTATTGTCTCATGAGCGGATACATATTTGAATGTATTTAGAAAAATAAACAAATAGGGGTTCCGCGCAGATGCATGCTAGCAGCATCGATCGTACGATGACGG CATTTCCCCGAAAAGTGCGATACTGACGCTACGATGCTACTACTGACGTCGTACCGCGATATATGCGCGTATCGCAGTACTACGCGCGCGATCGCATGACTGTGGG 7 Bioinformatics help you to see important patterns in large data sets Sequence databases  There are many excellent databases for DNA and amino acid sequence.  The best free database is GenBank,  organized by the National Center for Biotechnology Information (NCBI)  all non-proprietary sequence information ever collected  Synchronized daily with the DNA database of Japan and European Molecular biology laboratory 8 Practical Bioinformatics is taught at http://bioinf.moodlehub.com Other databases integrated within NCBI  PubMed and PubChem  Biomedical and Biochemical literature collections  BioSystems  Groups literature, small molecule and sequence data by biological relationship  PopSet  DNA sequences collated by phylogenetic relationship  Online Mendelian inheritance of man (OMIM)  Collates sequence information by disease process 9 Practical Bioinformatics is taught at http://bioinf.moodlehub.com Bioinformatics tools  Packages  MacVector for the Macintosh  PC packages  WWW  A mixed bag of programs that are generally compatible 10 Practical Bioinformatics is taught at http://bioinf.moodlehub.com Practical Bioinformatics lets you use the tools you already own. 11 Practical Bioinformatics is taught at http://bioinf.moodlehub.com Bioinformatics procedures  DNA sequence entry  Literature searches  Sequence downloads  Sequence comparison  Comparison to database  Sequence contribution  Restriction mapping  Genomic analysis  Multiple sequence alignment  Phylogenetic analysis  PCR primer design  Sequence manipulations  Protein property prediction 12 Practical Bioinformatics is taught at http://bioinf.moodlehub.com Topics  Databases and basic queries  Sequence comparison and alignment  Multiple sequence alignment and phylogenetics  Genomic analysis 13 Practical Bioinformatics is taught at http://bioinf.moodlehub.com NCBI Tools  PubMed  PubMed Central  My NCBI  GenBank  Entrez  BLAST  OMIM  Books  Taxonomy  Small molecules  Structure  Training  Software www.ncbi.nlm.nih.gov 14 Practical Bioinformatics is taught at http://bioinf.moodlehub.com Entrez global search  An NCBI search interface  Used to search  GenBank,protein databases  3-D protein structures database  Taxonomy database  Genomes databases  Population study databases  Chemical substance screening databases  Online books 15 Practical Bioinformatics is taught at http://bioinf.moodlehub.com Specialized Entrez search pages  Nucleotide  Protein  Genome 16 Practical Bioinformatics is taught at http://bioinf.moodlehub.com PubMed  A database and search tool of MEDLINE referenced literature  An excellent place to start a search  Highly cross-referenced to journals and other databases  Search by keyword, author, journal, gene name, etc. 17 Practical Bioinformatics is taught at http://bioinf.moodlehub.com PubMed search limits Narrow search by • Type of article • Species • Language • Gender • Age • Journal subset • Journal groups • Topic 18 Practical Bioinformatics is taught at http://bioinf.moodlehub.com GenBank • The repository for all non-proprietary sequence information ever collected • Well organized datasets • Excellent integrated tools for query and analysis • Cross-referenced to EMBL,DDBJ • More than one hundred million sequences 19 Practical Bioinformatics is taught at http://bioinf.moodlehub.com GenBank Search Results • Sequence category tabs • Gene database links • Organism chooser • List of matches Features 20 Practical Bioinformatics is taught at http://bioinf.moodlehub.com GenBank Search Results report  GenBank file  Analysis options  Related Articles  RefSeq  More information Features 21 Practical Bioinformatics is taught at http://bioinf.moodlehub.com GenBank file  Header  Locus  accession number  GI number  Length of sequence  Molecule type  Keywords  Source species  References 22 Practical Bioinformatics is taught at http://bioinf.moodlehub.com GenBank Links to PubMed Articles about the query sequence 23 Links to Gene  Gene/loci focused organization of data  RefSeqs  Genomic maps  Aliases  Functional summary  Related sequences in other species Report Table of Contents Links to other tools to analyze the query 24 Practical Bioinformatics is taught at http://bioinf.moodlehub.com Entrez Gene-RefSeqs Reference sequences (RefSeq) are the official sequence versions of your query. They are checked by NCBI staff for accuracy and completeness. Here are the mRNA (NM_) and Protein (NP_) RefSeqs. This query has two conserved domains There are large number of different versions of the genomic sequence from different large scale sequencing projects or slightly different versions. 25 Practical Bioinformatics is taught at http://bioinf.moodlehub.com Entrez Gene-Transcripts and Products Sequence viewer 26 Practical Bioinformatics is taught at http://bioinf.moodlehub.com Entrez Gene-GeneRIFs • GeneRIFs (References Into Function) are a very useful list of research articles that can give insight into the function of your query 27 Practical Bioinformatics is taught at http://bioinf.moodlehub.com Entrez Gene-Interactions and Markers This part of the report provides links to all known proteins that interact with your query and any genetic markers that can be used to study your query in populations. Sequence tagged sites (STS) are published PCR primer sets that can be used to locate the query within a large genomic region. 28 Entrez Gene-LinkOuts The last section is a series of links to external databases (non-NCBI). Some of these are very useful! iHOP (Information hyperlinked over proteins) is a great place to quickly review everything published about your query. From here you can buy research materials to study your query. 29 Exercise PubMed and Entrez  Goals  Search Pubmed  Get sequences using the Entrez browser  Become aquatinted with the links provided in the GenBank report  Open 2 browser windows  Follow Scenarios  Print out for later reference 30 Practical Bioinformatics is taught at http://bioinf.moodlehub.com