1. Essential Bioinformatics and Biocomputing Module (Tutorial) Biological Databases Lecturer: Chen Yuzong Jan 2003 TAs: Cao Zhiwei Lee Teckkwong, Bernett

2. Biological databases Tutorial outline Purpose: Extraction of relevant information for a particular macromolecule Case study: HLA-DRB1 molecule

3. Biological databases Case study: HLA-DR1 molecule Characterization of HLA-DR1 beta chain 1.Gene sequence 2.Gene structure: Introns, exons, promoter region 3.Protein sequence 4.Protein Sequence features and domains 5.Protein 3-D Structure 6.Function 7.Variation – closest variants in humans and other species 8.Clinical features

4. Clarification of Genetic information

5. Biological databases Case study: HLA-DR1 molecule HLA class II histocompatibility antigen, DR-1 beta chain Possible starting points a) GenBank b) SWISS-PROT http://www.expasy.orghttp://www.expasy.org (SWISS-PROT) Search by keyword “ HLA DR-1 ” Pick P13758

6. HLA-DRB1: Accession No. in Swiss-prot

7. HLA-DRB1: Swiss-prot entry

8. HLA-DRB1: Cross references

9. HLA-DRB1: Keywords

10. HLA-DR1 molecule: Function From SWISS-PROT Protein of the major histocompatibility complex (MHC) class II which is involved in the induction of strong immune reaction. MHC II is involved in the control the expression of surface structures on lymphocytes and macrophages.

11. HLA-DRB1: protein sequence features

12. HLA-DRB1: Protein sequence

14. Biological databases: Case study: HLA-DRB1 molecule By now we have studied SWISS-PROT entries. From these we can extract the specific information – colored red: 1.Gene sequence 2. Gene structure: Introns, exons, promoter region 3. Protein sequence 4. Protein Sequence features and domains 5. Protein 3-D Structure 6. Function 7.Variation – closest variants in humans and other species 8. Clinical features

15. HLA-DRB1 molecule (Genbank, follow the link) http://www3.ncbi.nlm.nih.gov/htbin-post/Entrez/query?db=n&form=6&dopt=g&uid=X03069 http://www3.ncbi.nlm.nih.gov/htbin-post/Entrez/query?db=n&form=6&dopt=g&uid=X03069

16. HLA-DR1 (Genbank): Gene structure (mRNA level)

17. HLA-DR1 (Genbank): Gene sequence (mRNA)

18. Map gene feature to RNA sequence tagttctccc tgagtgagac ttgcctgctt ctctggcccc tggtcctgtc ctgttctcca 60 gcatggtgtg tctgaagctc cctggaggct cctgcatgac agcgctgaca gtgacactga 120 tggtgctgag ctccccactg gctttggctg gggacacccg accacgtttc ttgtggcagc 180 ttaagtttga atgtcatttc ttcaatggga cggagcgggt gcggttgctg gaaagatgca 240 tctataacca agaggagtcc gtgcgcttcg acagcgacgt gggggagtac cgggcggtga 300 cggagctggg gcggcctgat gccgagtact ggaacagcca gaaggacctc ctggagcaga 360 ggcgggccgc ggtggacacc tactgcagac acaactacgg ggttggtgag agcttcacag 420 tgcagcggcg agttgagcct aaggtgactg tgtatccttc aaagacccag cccctgcagc 480 accacaacct cctggtctgc tctgtgagtg gtttctatcc aggcagcatt gaagtcaggt 540 ggttccggaa cggccaggaa gagaaggctg gggtggtgtc cacaggcctg atccagaatg 600 gagattggac cttccagacc ctggtgatgc tggaaacagt tcctcggagt ggagaggttt 660 acacctgcca agtggagcac ccaagtgtga cgagccctct cacagtggaa tggagagcac 720 ggtctgaatc tgcacagagc aagatgctga gtggagtcgg gggcttcgtg ctgggcctgc 780 tcttccttgg ggccgggctg ttcatctact tcaggaatca gaaaggacac tctggacttc 840 agccaacagg attcctgagc tgaaatgcag atgaccacat tcaaggaaga accttctgtc 900 ccagctttgc agaatgaaaa gctttcctgc ttggcagtta ttcttccaca agagagggct 960 ttctcaggac ctggttgcta ctggttcggc aactgcagaa aatgtcctcc cttgtggctt 1020 cctcagctcc tgcccttggc ctgaagtccc agcattgatg acagcgcctc atcttcaact 1080 tttgtgctcc cctttgccta aaccgtatgg cctcccgtgc atctgtactc accctgtacg 1140 acaaacacat tacattatta aatgtttctc aaagatggag tt 1182 Sig:63-149; exon1/2:162/163; exon2/3:432/433; exon3/4:741/715; exon4/5:825/826; Exon5/6:849/850

19. Searching intron from Genbank Eg. key words (HLA-DRB1*01 intron) http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=nucleotide&list_uids=1568491&dopt=GenBank http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=nucleotide&list_uids=1568491&dopt=GenBank X88793. H.sapiens HLA-DRB...[gi:1568491] LOCUS HSDRB101G 1332 bp DNA linear PRI 21-MAY-1996 DEFINITION H.sapiens HLA-DRB1*01 gene. ACCESSION X88793 VERSION X88793.1 GI:1568491 KEYWORDS HLA class II DR-beta chain; HLA-DRB1*01 gene. SOURCE human. ORGANISM Homo sapiens Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo. REFERENCE 1 (bases 1 to 1332) AUTHORS Svensson,A.C., Setterblad,N., Pihlgren,U., Rask,L. and Andersson,G. TITLE Evolutionary relationship between human major histocompatibility complex HLA-DR haplotypes JOURNAL Immunogenetics 43 (5), 304-314 (1996) MEDLINE 96175156 PUBMED 9110934 REFERENCE 2 (bases 1 to 1332) AUTHORS Svensson,A.C. TITLE Direct Submission JOURNAL Submitted (19-JUN-1995) A.C. Svensson, Swedish University of Agric. Sciences, Dept of Cell Research, Genetic Center, Box 7055, 750 07 Uppsala, SWEDEN FEATURES Location/Qualifiers source 1..1332 /organism="Homo sapiens" /db_xref="taxon:9606" /chromosome="6" /haplotype="DR1/1"

20. X88793. H.sapiens HLA-DRB...[gi:1568491] (cotinued) FEATURES Location/Qualifiers source 1..1332 /organism="Homo sapiens" /db_xref="taxon:9606" /chromosome="6" /haplotype="DR1/1" intron <1..469 /number=4 gene 470..493 /gene="HLA-DRB1*01" CDS 493 /gene="HLA-DRB1*01" /codon_start=1 /product="HLA class II DR-beta chain" /protein_id="CAA61272.1" /db_xref="GI:1568492" /db_xref="SPTREMBL:Q29797" /translation="DTLDFSQQ" exon 470..493 /gene="HLA-DRB1*01" /number=5 intron 494..>1332 /number=5 LTR 540..1053 /note="ERV9 LTR"

21. Searching promoter from Genbank Eg. key words (HLA-DRB1 promoter)

23. Biological databases: Case study: HLA-DRB1 molecule By now we have studied SWISS-PROT and Genbank entries. From these we can extract the specific information – colored red: 1.Gene sequence 2. Gene structure: Introns, exons, promoter region 3. Protein sequence 4. Protein Sequence features and domains 5. Protein Structure 6. Function 7.Variation – closest variants in humans and other species 8. Clinical features

24. Protein strucutre: Follow Swiss-prot link to PDB (Eg. PDBID 1DLH) http://www.rcsb.org/pdb/cgi/explore.cgi?pid=2031041686850&page=0&pdbId=1DLH http://www.rcsb.org/pdb/cgi/explore.cgi?pid=2031041686850&page=0&pdbId=1DLH Crystal structure of the human class II MHC protein HLA-DR1 complexed with an influenza virus peptide.

25. HLA-DRB1: Variation – closest variants in humans Keyword: HLA-DRB1 variant search against Genbank or swissprot 68 hits in Genbank on 04/01/2003 21:43pm. 1 hit in Swiss-prot at the same time. http://tw.expasy.org/cgi-bin/niceprot.pl?Q30112 The No. of matching list may vary because of database updating.

26. HLA-DRB1: Variation – closest variants in other species Try keywords Use sequence similarity search

27. HLA-DRB1 molecule: Clinical features This entry has no links to the OMIM database, we will resort to searching literature databases. http://www3.ncbi.nlm.nih.gov/Entrez/ http://www3.ncbi.nlm.nih.gov/Entrez/

28. Summary Genebank Swiss-prot PDB Pubmed Others