Bioinformatika pro PřfUK 2001

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Bioinformatika pro PfUK 2001. Ji Vondrek stav organick chemie a biochemie vondrasek@uochb.cas.cz. Jan Paes stav molekulrn genetiky hpaces@img.cas.cz. http://bio.img.cas.cz/PrfUK2002. Databze: obsah. principy SQL formty biologickch sekvenc IUB kdy DNA databze - PowerPoint PPT Presentation

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<ul><li><p>Jan Paesstav molekulrn genetikyhpaces@img.cas.czJi Vondrekstav organick chemie a biochemievondrasek@uochb.cas.czhttp://bio.img.cas.cz/PrfUK2002Bioinformatikapro PfUK 2001</p></li><li><p>Databze: obsahprincipySQLformty biologickch sekvencIUB kdyDNA databzeproteinov a genomov databzestrukturn databze</p></li><li><p>organizace databzRelan databze</p><p>c_ididentifiktor, slotitletextjournalkrtk textyeardatum</p><p>a_ididentifiktorc_ididentifiktornamekrtk text</p><p>k_ididentifiktorc_ididentifiktorkeywordkrtk text</p></li><li><p>SQL: Structured Query LanguageCREATE TABLE article (c_idINTEGER,titleTEXT,journalVARCHAR(30),yearDATE);</p><p>c_ididentifiktor, slotitletextjournalkrtk textyeardatum</p></li><li><p>SQL: Structured Query LanguageCREATE TABLE author (a_idINTEGER,c_idINTEGER,nameVARCHAR(30));</p><p>a_ididentifiktorc_ididentifiktornamekrtk text</p></li><li><p>SQL: Structured Query LanguageINSERT INTO article SET c_id='1',title='Something absolutely fantastic',journal='Bioinformatics',year='2002';</p><p>INSERT INTO author SETa_id='1',c_id='1',name='Paces, Jan';</p><p>INSERT INTO author SETa_id='2',c_id='1',name='Vondrasek, Jiri';</p></li><li><p>SQL: Structured Query LanguageSELECT article.title,article.journal,author.nameFROM article,journalWHERE article.c_id = author.c_id ANDarticle.year &gt; '2000' ANDauthor.name LIKE 'Paces%';</p></li><li><p>nukleotidyaminokyselinyIUB kdy</p><p>kdnukleotidykomplementAATCCGGGCTTA(UU)AMACKRAGYWATSSCGWYCTRKGTMVACGBHACTDDAGTHBCGTVNACGTN-mezera-</p><p>kdtpsmenn kd aminokyselinaAAlaalaninCCyscysteinDAspasparagov kyselinaGGluglutamov kyselinaHHishistidinIIleisoleucinKLyslysinLLeuleucinMMetmethioninNAsnasparaginPProprolinQGlnglutaminRArgargininSSerserinTThrthreoninVValvalinWTrptryptofanYTyrtyrosinBAsxasparagov kys. nebo asparaginZGlxglutamov kys. nebo glutaminXXxxjakkoliv aminokyselina*---stop</p></li><li><p>binrns chromatogramy</p><p>pro programyminimln</p><p>anotovantextovSCFALFABI</p><p>intern formty databztextfasta</p><p>EMBLGenBankASNXMLformty sekvenc</p></li><li><p>SCF (standart chromatogram file)formty sekvenc - SCF</p></li><li><p>EMBL (formt databze EMBL)ID AF031150 standard; RNA; ROD; 1379 BP. XX AC AF031150; XX SV AF031150.1 XX DT 27-FEB-1998 (Rel. 54, Created) DT 27-FEB-1998 (Rel. 54, Last updated, Version 1) XX DE Mus musculus paired-box transcription factor (Pax4) mRNA, complete cds. XX KW . XX OS Mus musculus (house mouse) OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; OC Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Mus. XX RN [1] RP 1-1379 RA 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 its RT human homologue; RL Biochem. Biophys. Res. Commun. 243:628-633(1998). XX RN [2] RP 1-1379 RA 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, Japan XX FH Key Location/Qualifiersformty sekvenc - EMBL</p></li><li><p>FH Key Location/Qualifiers FH FT source 1..1379 FT /db_xref=taxon:10090FT /organism=Mus musculus FT /cell_line=MIN6 FT CDS 297..1346 FT /codon_start=1 FT /gene=Pax4 FT /product=paired-box transcription factor FT /protein_id=AAC40046.1 FT /translation=MQQDGLSSVNQLGGLFVNGRPLPLDTRQQIVQLAIRGMRPCDISR FT SLKVSNGCVSKILGRYYRTGVLEPKCIGGSKPRLATPAVVARIAQLKDEYPALFAWEIQ FT HQLCTEGLCTQDKAPSVSSINRVLRALQEDQSLHWTQLRSPAVLAPVLPSPHSNCGAPR FT GPHPGTSHRNRTIFSPGQAEALEKEFQRGQYPDSVARGKLAAATSLPEDTVRVWFSNRR FT AKWRRQEKLKWEAQLPGASQDLTVPKNSPGIISAQQSPGSVPSAALPVLEPLSPSFCQL FT CCGTAPGRCSSDTSSQAYLQPYWDCQSLLPVASSSYVEFAWPCLTTHPVHHLIGGPGQV FT PSTHCSNWP XX SQ 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 //EMBL (formt databze EMBL)formty sekvenc - EMBL</p></li><li><p>GenbankLOCUS AF145233 1360 bp mRNA ROD 23-OCT-1999 DEFINITION Mus musculus transcription factor PAX4 (Pax4) mRNA, complete cds. ACCESSION AF145233 VERSION AF145233.1 GI:6102607 KEYWORDS . 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 10364449 REFERENCE 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 Republic FEATURES 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" formty sekvenc - GenBank</p></li><li><p>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 t ORIGIN 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 //</p><p>Genbankformty sekvenc - GenBank</p></li><li><p>fasta&gt;gi|6102607|gb|AF145233.1|AF145233 Mus musculus transcription factor PAX4 (Pax4) mRNA, complete cds TGGCAGGACTGAAGCAGCTGGAGGCTGTTACAAGACCAGACCACCAGCAAACCCTGGAGCCTGCACAGGA CCCTGAGACCTCTTCCTGGAATTCCCACCTTTTTTCCTCCATCCAGAACCAGTCCCAAAGAGAAACTTCC AGAAGGAGCTCTCCGTTTTCAGTTTGCCAGTTGGCTTCCTGTCCTTCTGTGAGGAGTACCAGTGTGAAGC ATGCAGCAGGACGGACTCAGCAGTGTGAATCAGCTAGGGGGACTCTTTGTGAATGGCCGGCCCCTTCCTC TGGACACCAGGCAGCAGATTGTGCAGCTAGCAATAAGAGGGATGCGACCCTGTGACATTTCACGGAGCCT TAAGGTATCTAATGGCTGTGTGAGCAAGATCCTAGGACGCTACTACCGCACAGGTGTCTTGGAACCCAAG TGTATTGGGGGAAGCAAACCACGTCTGGCCACACCTGCTGTGGTGGCTCGAATTGCCCAGCTAAAGGATG AGTACCCTGCTCTTTTTGCCTGGGAGATCCAACACCAGCTTTGCACTGAAGGGCTTTGTACCCAGGACAA GGCTCCCAGTGTGTCCTCTATCAATCGAGTACTTCGGGCACTTCAGGAAGACCAGAGCTTGCACTGGACT CAACTCAGATCACCAGCTGTGTTGGCTCCAGTTCTTCCCAGTCCCCACAGTAACTGTGGGGCTCCCCGAG GCCCCCACCCAGGAACCAGCCACAGGAATCGGACTATCTTCTCCCCGGGACAAGCCGAGGCACTGGAGAA AGAGTTTCAGCGTGGGCAGTATCCAGATTCAGTGGCCCGTGGGAAGCTGGCTGCTGCCACCTCTCTGCCT GAAGACACGGTGAGGGTTTGGTTTTCTAACAGAAGAGCCAAATGGCGCAGGCAAGAGAAGCTGAAATGGG AAGCACAGCTGCCAGGTGCTTCCCAGGACCTGACAGTACCAAAAAATTCTCCAGGGATCATCTCTGCACA GCAGTCCCCCGGCAGTGTACCCTCAGCTGCCTTGCCTGTGCTGGAACCATTGAGTCCTTCCTTCTGTCAG CTATGCTGTGGGACAGCACCAGGCAGATGTTCCAGTGACACCTCATCCCAGGCCTATCTCCAACCCTACT GGGACTGCCAATCCCTCCTTCCTGTGGCTTCCTCCTCATATGTGGAATTTGCCTGGCCCTGCCTCACCAC CCATCCTGTGCATCATCTGATTGGAGGCCCAGGACAAGTGCCATCAACCCATTGCTCAAACTGGCCATAA GAGGCCTCTATTTGACAGTAATAAAAACCTTTTCTTAGATGTTAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAformty sekvenc - FastA</p></li><li><p>ASNSeq-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 </p><p>formty sekvenc - ASN</p></li><li><p>Bioinformatic Links</p></li><li><p>GenBank</p></li><li><p>Swiss-Prot</p></li><li><p>EntrezEntrezLiterature (PubMed)Nucleotide (GenBank)Protein (PIR)GenomeStructure (PDB)PopSetTaxonomyOMIM</p></li><li><p>Entrez</p></li><li><p>Entrez</p></li><li><p>Entrez</p></li><li><p>SRS</p></li><li><p>SRS</p></li><li><p>SRS</p></li><li><p>SRS</p></li><li><p>SRS</p></li><li><p>SRS</p></li><li><p>SRS</p></li><li><p>SRS - list</p></li><li><p>SRS - list</p></li><li><p>SRS - list</p></li><li><p>PDB</p></li><li><p>PDB</p></li><li><p>PDB</p></li><li><p>PDBHEADER 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 </p></li><li><p>PDBSEQRES 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...</p></li></ul>