Bioinformatika pro PřfUK 2001

1. Bioinformatikapro PřfUK 2001 Jiří Vondrášek Ústav organické chemie a biochemie vondrasek@uochb.cas.cz Jan Pačes Ústav molekulární genetiky hpaces@img.cas.cz http://bio.img.cas.cz/PrfUK2002

2. Databáze: obsah principy SQL formáty biologických sekvencí IUB kódy DNA databáze proteinové a genomové databáze strukturní databáze

3. organizace databází Relační databáze

4. SQL: Structured Query Language CREATE TABLE article ( c_id INTEGER, title TEXT, journal VARCHAR(30), year DATE );

5. SQL: Structured Query Language CREATE TABLE author ( a_id INTEGER, c_id INTEGER, name VARCHAR(30) );

6. SQL: Structured Query Language INSERT INTO article SET c_id = '1', title = 'Something absolutely fantastic', journal = 'Bioinformatics', year = '2002'; INSERT INTO author SET a_id = '1', c_id = '1', name = 'Paces, Jan'; INSERT INTO author SET a_id = '2', c_id = '1', name = 'Vondrasek, Jiri';

7. SQL: Structured Query Language SELECT article.title,article.journal,author.name FROM article,journal WHERE article.c_id = author.c_id AND article.year > '2000' AND author.name LIKE 'Paces%';

8. IUB kódy nukleotidy aminokyseliny

9. formáty sekvencí binární s chromatogramy pro programy SCF ALF ABI interní formáty databází textové minimální anotované text fasta EMBL GenBank ASN XML

10. formáty sekvencí - SCF SCF (standart chromatogram file)

11. formáty sekvencí - EMBL EMBL (formát databáze EMBL) ID AF031150 standard; RNA; ROD; 1379 BP.XXAC AF031150;XXSV AF031150.1XXDT 27-FEB-1998 (Rel. 54, Created)DT 27-FEB-1998 (Rel. 54, Last updated, Version 1)XXDE Mus musculus paired-box transcription factor (Pax4) mRNA, complete cds.XXKW .XXOS Mus musculus (house mouse)OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;OC Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Mus.XXRN [1]RP 1-1379RA Inoue H., Nomiyama J., Nakai K., Matsutani A., Tanizawa Y., Oka Y.;RT Isolation of full-length cDNA of mouse PAX4 gene and identification of itsRT human homologue;RL Biochem. Biophys. Res. Commun. 243:628-633(1998).XXRN [2]RP 1-1379RA Inoue H., Nomiyama J., Nakai K., Tanizawa Y., Oka Y.;RT ;RL Submitted (23-OCT-1997) to the EMBL/GenBank/DDBJ databases.RL Third Dept. of Int. Med., Yamaguchi University, 1144 Kogushi, Ube,RL Yamaguchi 755, JapanXXFH Key Location/Qualifiers …

12. formáty sekvencí - EMBL EMBL (formát databáze EMBL) … FH Key Location/QualifiersFHFT source 1..1379FT /db_xref=taxon:10090 FT /organism=Mus musculusFT /cell_line=MIN6FT CDS 297..1346FT /codon_start=1FT /gene=Pax4FT /product=paired-box transcription factorFT /protein_id=AAC40046.1FT /translation=MQQDGLSSVNQLGGLFVNGRPLPLDTRQQIVQLAIRGMRPCDISRFT SLKVSNGCVSKILGRYYRTGVLEPKCIGGSKPRLATPAVVARIAQLKDEYPALFAWEIQFT HQLCTEGLCTQDKAPSVSSINRVLRALQEDQSLHWTQLRSPAVLAPVLPSPHSNCGAPRFT GPHPGTSHRNRTIFSPGQAEALEKEFQRGQYPDSVARGKLAAATSLPEDTVRVWFSNRRFT AKWRRQEKLKWEAQLPGASQDLTVPKNSPGIISAQQSPGSVPSAALPVLEPLSPSFCQLFT CCGTAPGRCSSDTSSQAYLQPYWDCQSLLPVASSSYVEFAWPCLTTHPVHHLIGGPGQVFT PSTHCSNWPXXSQ Sequence 1379 BP; 327 A; 402 C; 347 G; 303 T; 0 other; aaaaaaaaaa aaaaagcggc cgctgaattc tagcagaagg ctgccctctg ctcctgagtg 60 aaggctctgt gaagctctgg accccctggc aggactgaag cagctggagg ctgttacaag 120 accagaccac cagcaaaccc tggagcctgc acaggaccct gagacctctt cctggaattc 180 ccaccttttt tcctccatcc agaaccagtc ccaaagagaa acttccagaa ggagctctcc 240 gttttcagtt tgccagttgg cttcctgtcc ttctgtgagg agtaccagtg tgaagcatgc 300 agcaggacgg actcagcagt gtgaatcagc tagggggact ctttgtgaat ggccggcccc 360… gctgtgggac agcaccaggc agatgttcca gtgacacctc atcccaggcc tatctccaac 1200 cctactggga ctgccaatcc ctccttcctg tggcttcctc ctcatatgtg gaatttgcct 1260 ggccctgcct caccacccat cctgtgcatc atctgattgg aggcccagga caagtgccat 1320 caacccattg ctcaaactgg ccataagagg cctctatttg acagtaataa aaacctttt 1379//

13. formáty sekvencí - GenBank Genbank LOCUS AF145233 1360 bp mRNA ROD 23-OCT-1999DEFINITION Mus musculus transcription factor PAX4 (Pax4) mRNA, complete cds.ACCESSION AF145233VERSION AF145233.1 GI:6102607KEYWORDS .SOURCE house mouse. ORGANISM Mus musculus Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Mus.REFERENCE 1 (bases 1 to 1360) AUTHORS Kalousova,A., Benes,V., Paces,J., Paces,V. and Kozmik,Z. TITLE DNA binding and transactivating properties of the paired and homeobox protein Pax4 JOURNAL Biochem. Biophys. Res. Commun. 259 (3), 510-518 (1999) MEDLINE 99294619 PUBMED 10364449REFERENCE 2 (bases 1 to 1360) AUTHORS Kalousova,A., Paces,J. and Kozmik,Z. TITLE Direct Submission JOURNAL Submitted (23-APR-1999) Dept. of Transcription Regulation, Institute of Molecular Genetics, Videnska 1083, Prague 142 20, Czech RepublicFEATURES Location/Qualifiers source 1..1360 /organism="Mus musculus" /db_xref="taxon:10090" gene 1..1360 /gene="Pax4" CDS 211..1260 /gene="Pax4" /note="DNA binding protein; paired box protein; homeobox protein" /codon_start=1 /product="transcription factor PAX4" /protein_id="AAF03533.1"…

14. formáty sekvencí - GenBank Genbank CDS 211..1260 /gene="Pax4" /note="DNA binding protein; paired box protein; homeobox protein" /codon_start=1 /product="transcription factor PAX4" /protein_id="AAF03533.1" /db_xref="GI:6102608" /translation="MQQDGLSSVNQLGGLFVNGRPLPLDTRQQIVQLAIRGMRPCDIS RSLKVSNGCVSKILGRYYRTGVLEPKCIGGSKPRLATPAVVARIAQLKDEYPALFAWE IQHQLCTEGLCTQDKAPSVSSINRVLRALQEDQSLHWTQLRSPAVLAPVLPSPHSNCG APRGPHPGTSHRNRTIFSPGQAEALEKEFQRGQYPDSVARGKLAAATSLPEDTVRVWF SNRRAKWRRQEKLKWEAQLPGASQDLTVPKNSPGIISAQQSPGSVPSAALPVLEPLSP SFCQLCCGTAPGRCSSDTSSQAYLQPYWDCQSLLPVASSSYVEFAWPCLTTHPVHHLI GGPGQVPSTHCSNWP"BASE COUNT 359 a 381 c 328 g 292 tORIGIN 1 tggcaggact gaagcagctg gaggctgtta caagaccaga ccaccagcaa accctggagc 61 ctgcacagga ccctgagacc tcttcctgga attcccacct tttttcctcc atccagaacc 121 agtcccaaag agaaacttcc agaaggagct ctccgttttc agtttgccag ttggcttcct 181 gtccttctgt gaggagtacc agtgtgaagc atgcagcagg acggactcag cagtgtgaat… 1081 tccagtgaca cctcatccca ggcctatctc caaccctact gggactgcca atccctcctt 1141 cctgtggctt cctcctcata tgtggaattt gcctggccct gcctcaccac ccatcctgtg 1201 catcatctga ttggaggccc aggacaagtg ccatcaaccc attgctcaaa ctggccataa 1261 gaggcctcta tttgacagta ataaaaacct tttcttagat gttaaaaaaa aaaaaaaaaa 1321 aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa //

15. formáty sekvencí - FastA fasta >gi|6102607|gb|AF145233.1|AF145233 Mus musculus transcription factor PAX4 (Pax4) mRNA, complete cdsTGGCAGGACTGAAGCAGCTGGAGGCTGTTACAAGACCAGACCACCAGCAAACCCTGGAGCCTGCACAGGACCCTGAGACCTCTTCCTGGAATTCCCACCTTTTTTCCTCCATCCAGAACCAGTCCCAAAGAGAAACTTCCAGAAGGAGCTCTCCGTTTTCAGTTTGCCAGTTGGCTTCCTGTCCTTCTGTGAGGAGTACCAGTGTGAAGCATGCAGCAGGACGGACTCAGCAGTGTGAATCAGCTAGGGGGACTCTTTGTGAATGGCCGGCCCCTTCCTCTGGACACCAGGCAGCAGATTGTGCAGCTAGCAATAAGAGGGATGCGACCCTGTGACATTTCACGGAGCCTTAAGGTATCTAATGGCTGTGTGAGCAAGATCCTAGGACGCTACTACCGCACAGGTGTCTTGGAACCCAAGTGTATTGGGGGAAGCAAACCACGTCTGGCCACACCTGCTGTGGTGGCTCGAATTGCCCAGCTAAAGGATGAGTACCCTGCTCTTTTTGCCTGGGAGATCCAACACCAGCTTTGCACTGAAGGGCTTTGTACCCAGGACAAGGCTCCCAGTGTGTCCTCTATCAATCGAGTACTTCGGGCACTTCAGGAAGACCAGAGCTTGCACTGGACTCAACTCAGATCACCAGCTGTGTTGGCTCCAGTTCTTCCCAGTCCCCACAGTAACTGTGGGGCTCCCCGAGGCCCCCACCCAGGAACCAGCCACAGGAATCGGACTATCTTCTCCCCGGGACAAGCCGAGGCACTGGAGAAAGAGTTTCAGCGTGGGCAGTATCCAGATTCAGTGGCCCGTGGGAAGCTGGCTGCTGCCACCTCTCTGCCTGAAGACACGGTGAGGGTTTGGTTTTCTAACAGAAGAGCCAAATGGCGCAGGCAAGAGAAGCTGAAATGGGAAGCACAGCTGCCAGGTGCTTCCCAGGACCTGACAGTACCAAAAAATTCTCCAGGGATCATCTCTGCACAGCAGTCCCCCGGCAGTGTACCCTCAGCTGCCTTGCCTGTGCTGGAACCATTGAGTCCTTCCTTCTGTCAGCTATGCTGTGGGACAGCACCAGGCAGATGTTCCAGTGACACCTCATCCCAGGCCTATCTCCAACCCTACTGGGACTGCCAATCCCTCCTTCCTGTGGCTTCCTCCTCATATGTGGAATTTGCCTGGCCCTGCCTCACCACCCATCCTGTGCATCATCTGATTGGAGGCCCAGGACAAGTGCCATCAACCCATTGCTCAAACTGGCCATAAGAGGCCTCTATTTGACAGTAATAAAAACCTTTTCTTAGATGTTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

16. formáty sekvencí - ASN ASN Seq-entry ::= set { class nuc-prot , descr { title "Mus musculus transcription factor PAX4 (Pax4) mRNA, complete cds." , source { org { taxname "Mus musculus" , common "house mouse" , db { { db "taxon" , tag id 10090 } } , orgname { name binomial { genus "Mus" , species "musculus" } , lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Mus" , gcode 1 , mgcode 2 , div "ROD" } } } , pub { pub { sub { authors { names std

17. Bioinformatic Links

18. GenBank

19. Swiss-Prot

20. Entrez • Entrez • Literature (PubMed) • Nucleotide (GenBank) • Protein (PIR) • Genome • Structure (PDB) • PopSet • Taxonomy • OMIM

21. Entrez

22. Entrez

23. Entrez

24. SRS

25. SRS

26. SRS

27. SRS

28. SRS

29. SRS

30. SRS

31. SRS - list

32. SRS - list

33. SRS - list

34. PDB

35. PDB

36. PDB

37. PDB HEADER GENE REGULATION/DNA 22-APR-99 6PAX TITLE CRYSTAL STRUCTURE OF THE HUMAN PAX-6 PAIRED DOMAIN-DNA TITLE 2 COMPLEX REVEALS A GENERAL MODEL FOR PAX PROTEIN-DNA TITLE 3 INTERACTIONS COMPND MOL_ID: 1; COMPND 2 MOLECULE: HOMEOBOX PROTEIN PAX-6; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 BIOLOGICAL_UNIT: MONOMER; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 26 NUCLEOTIDE DNA; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES; COMPND 10 BIOLOGICAL_UNIT: MONOMER; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: 26 NUCLEOTIDE DNA; COMPND 13 CHAIN: C; COMPND 14 ENGINEERED: YES; COMPND 15 BIOLOGICAL_UNIT: MONOMER SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 GENE: PAX6; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 MOL_ID: 3; SOURCE 10 SYNTHETIC: YES KEYWDS PAX, PAIRED DOMAIN, TRANSCRIPTION, PROTEIN-DNA INTERACTIONS, KEYWDS 2 GENE REGULATION/DNA EXPDTA X-RAY DIFFRACTION AUTHOR H.E.XU,M.A.ROULD,W.XU,J.A.EPSTEIN,R.L.MAAS,C.O.PABO REVDAT 1 13-JUL-99 6PAX 0 JRNL AUTH H.E.XU,M.A.ROULD,W.XU,J.A.EPSTEIN,R.L.MAAS,C.O.PABO JRNL TITL CRYSTAL STRUCTURE OF THE HUMAN PAX-6 PAIRED JRNL TITL 2 DOMAIN-DNA COMPLEX REVEALS SPECIFIC ROLES FOR THE JRNL TITL 3 LINKER REGION AND THE CARBOXY-TERMINAL SUBDOMAIN JRNL TITL 4 IN DNA BINDING

38. PDB SEQRES 1 A 133 SER HIS SER GLY VAL ASN GLN LEU GLY GLY VAL PHE VAL SEQRES 2 A 133 ASN GLY ARG PRO LEU PRO ASP SER THR ARG GLN ARG ILE SEQRES 3 A 133 VAL GLU LEU ALA HIS SER GLY ALA ARG PRO CYS ASP ILE SEQRES 4 A 133 SER ARG ILE LEU GLN VAL SER ASN GLY CYS VAL SER LYS SEQRES 5 A 133 ILE LEU GLY ARG TYR TYR ALA THR GLY SER ILE ARG PRO SEQRES 6 A 133 ARG ALA ILE GLY GLY SER LYS PRO ARG VAL ALA THR PRO SEQRES 7 A 133 GLU VAL VAL SER LYS ILE ALA GLN TYR LYS GLN GLU CYS SEQRES 8 A 133 PRO SER ILE PHE ALA TRP GLU ILE ARG ASP ARG LEU LEU SEQRES 9 A 133 SER GLU GLY VAL CYS THR ASN ASP ASN ILE PRO SER VAL SEQRES 10 A 133 SER SER ILE ASN ARG VAL LEU ARG ASN LEU ALA SER GLU SEQRES 11 A 133 LYS GLN GLN SEQRES 1 B 26 A A G C A T T T T C A C G SEQRES 2 B 26 C A T G A G T G C A C A G SEQRES 1 C 26 T T C T G T G C A C T C A SEQRES 2 C 26 T G C G T G A A A A T G C FORMUL 4 HOH *84(H2 O1) HELIX 1 1 ASP A 20 HIS A 31 1 12 HELIX 2 2 PRO A 36 LEU A 43 1 8 HELIX 3 3 ASN A 47 THR A 60 1 14 HELIX 4 4 PRO A 78 GLU A 90 1 13 HELIX 5 5 ALA A 96 SER A 105 1 10 HELIX 6 6 VAL A 117 GLU A 130 1 14 SHEET 1 A 2 SER A 3 VAL A 5 0 SHEET 2 A 2 VAL A 11 VAL A 13 -1 N PHE A 12 O GLY A 4 CRYST1 33.840 61.686 171.111 90.00 90.00 90.00 P 21 21 21 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.029551 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016211 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005844 0.00000 ATOM 1 N SER A 1 -1.985 -12.356 81.201 1.00 60.11 N ATOM 2 CA SER A 1 -1.709 -12.440 82.636 1.00 60.41 C ATOM 3 C SER A 1 -2.774 -13.282 83.373 1.00 59.35 C ATOM 4 O SER A 1 -3.734 -13.763 82.751 1.00 58.16 O ATOM 5 CB SER A 1 -1.638 -11.029 83.229 1.00 64.08 C ATOM 6 OG SER A 1 -2.862 -10.345 83.045 1.00 69.46 O ATOM 7 H SER A 1 -2.431 -11.538 80.917 1.00 40.00 H ATOM 8 HG SER A 1 -2.887 -9.549 83.596 1.00 40.00 H ATOM 9 N HIS A 2 -2.634 -13.393 84.701 1.00 59.45 N

39. SCOP

40. PDBsum

41. PDBsum

42. PDBsum

43. CATH

44. CATH

45. FSSP - Fold classification

46. Structural genomics

47. Bioinformatické WWW rozcestníky EBI: http://www.ebi.ac.uk/Tools Expasy: http://www.expasy.ch Pasteur: http://bioweb.pasteur.fr Lyon: http://pbil.univ-lyon1.fr NCBI: http://ncbi.nlm.nih.gov

48. EBI

49. ExPASy

50. PBIL