Advanced NCBI

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Course NCBI / Entrez Web-Services Blast XML, XSLT, LINUX, Bioinformatics
Université de Nantes France
25 Sept 2013

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Advanced NCBI

  1. 1. Advanced NCBI. The Entrez API https://github.com/lindenb/courses Pierre Lindenbaum @yokofakun pierre.lindenbaum@univ-nantes.fr http://plindenbaum.blogspot.com Institut du Thorax. Nantes. France September 19, 2014 Pierre Lindenbaum@yokofakun pierre.lindenbaum@univ-nantes.fr httAp:d/v/apnlciedndNenCbBaIu.Tm.hbelEongtsrpeoztA.cPoIhmttps://github.com/lindenb/courses
  2. 2. NCBI ? What about EBI, ENSEMBL, ... Pierre Lindenbaum@yokofakun pierre.lindenbaum@univ-nantes.fr httAp:d/v/apnlciedndNenCbBaIu.Tm.hbelEongtsrpeoztA.cPoIhmttps://github.com/lindenb/courses
  3. 3. Pierre Lindenbaum@yokofakun pierre.lindenbaum@univ-nantes.fr httAp:d/v/apnlciedndNenCbBaIu.Tm.hbelEongtsrpeoztA.cPoIhmttps://github.com/lindenb/courses
  4. 4. What will be covered today? : File formats... EInfo, GQuery, ESearch , Esummary, EFetch.. processing XML answer with XSLT: HTML, SVG, R... generating a java parser for dbSNP. NCBI EBot using standalone BLAST Pierre Lindenbaum@yokofakun pierre.lindenbaum@univ-nantes.fr httAp:d/v/apnlciedndNenCbBaIu.Tm.hbelEongtsrpeoztA.cPoIhmttps://github.com/lindenb/courses
  5. 5. CURL c u r l " ht tp : / / en . wi k i p e d i a . org / wi k i /Main page " Pierre Lindenbaum@yokofakun pierre.lindenbaum@univ-nantes.fr httAp:d/v/apnlciedndNenCbBaIu.Tm.hbelEongtsrpeoztA.cPoIhmttps://github.com/lindenb/courses
  6. 6. XML Pierre Lindenbaum@yokofakun pierre.lindenbaum@univ-nantes.fr httAp:d/v/apnlciedndNenCbBaIu.Tm.hbelEongtsrpeoztA.cPoIhmttps://github.com/lindenb/courses
  7. 7. XSLT Pierre Lindenbaum@yokofakun pierre.lindenbaum@univ-nantes.fr httAp:d/v/apnlciedndNenCbBaIu.Tm.hbelEongtsrpeoztA.cPoIhmttps://github.com/lindenb/courses
  8. 8. XSLTPROC x s l t p r o c s t y l e s h e e t . x s l f i l e . xml > r e s u l t . xml Pierre Lindenbaum@yokofakun pierre.lindenbaum@univ-nantes.fr httAp:d/v/apnlciedndNenCbBaIu.Tm.hbelEongtsrpeoztA.cPoIhmttps://github.com/lindenb/courses
  9. 9. Formats Pierre Lindenbaum@yokofakun pierre.lindenbaum@univ-nantes.fr httAp:d/v/apnlciedndNenCbBaIu.Tm.hbelEongtsrpeoztA.cPoIhmttps://github.com/lindenb/courses
  10. 10. Formats Genbank http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch. fcgi?db=nucleotide&id=25&rettype=gb LOCUS X53813 422 bp DNA l i n e a r MAM 22

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