Bioinformatics Practical for Biochemists

Transcription

1 Bioinformatics Practical for Biochemists Andrei Lupas, Birte Höcker, Steffen Schmidt WS 2013/2014!! 01. DNA Tutorial - notebook / DBs / genome browser / translation

2 Electronic Lab notebook like in a wet-lab you need to keep track of what you re doing you want to write your findings / annotation of a sequence down Advanced Word processors enable you to highlight and/or color sequences rectangular selection of text in e.g. an alignment to highlight these

3 Main resources of sequences NCBI (National Center for Biotechnology Information) GenBank as main resource for DNA Common Search Fields [gene] [orgn] [accn] [auth] [titl] EBI (National Center for Biotechnology Information) EMBL as main resource for DNA Always record the accession number of your sequence

4 Dedicated Genome Databases used to be easy now sequencing is cheap personalized genome!

5 Genome Browser GUI for display of information from a biological database for genomic data Visualise & Browse entire genomes with annotated data gene prediction / structure expression regulation variation comparative analysis epigenetic data

6 Genome Browser The SEED Viewer

7 pubseed.theseed.org

8 seed-viewer.theseed.org

9 The SEED: genome information

10 The SEED: genome information

11 pubseed.theseed.org

12 seed-viewer.theseed.org

13 UCSC Genome Browser

14 UCSC Genome Browser Get DNA / Screen

15 UCSC Genome Browser Tracks with annotation information

16 UCSC Genome Browser

17 Getting the code incl. start & stop codons Alternative start codon AUG (83%) GUG (14%) UUG (3%)! Alternative stops UAA (63%, ochre ) UGA (29% opal ) / or Sec (Selenoncys) UAG (8%, amber ) E. coli 17

18 AT C G G A T C TGA0 T1 G2 RBS & Start in E. coli E. coli Ribosome binding sites C GTA GC TA C TA GAT CG C TGA C TGA C T A G G CA G A T TC C TAG C TGA C GAT TA C GTA CG G T C A GC AT G C TGA G A C C AT TG C A TG C TA G C TA Schneider & Stephens, 1990, NAR

19 Universal Code Differences in Species Arginine Human Drosophila E. coli AGA 22% 10% 1% AGG 23% 6% 1% CGA 10% 8% 4% CGC 22% 49% 39% CGG 14% 9% 4% CGU 9% 18% 49% Codon Usage Database,

20 Universal Code Difference H. sapiens Codon Standard code Mitochondrial" code UGA Stop Trp UGG Trp Trp AUA Ile Met AUG Met Met AGA Arg Stop AGG Arg Stop Stryer, Biochemistry

21 Promotor Structure - Plasmid Sty I(57) Bpu1102 I(80) Ava I(158) Xho I(158) Not I(166) Eag I(166) Hind III(173) Sal I(179) Sac I(190) EcoR I(192) BamH I(198) Dra III(5201) f1 origin ( ) Nhe I(231) Nde I(238) Xba I(276) Bgl II(342) SgrA I(383) Sph I(539) EcoN I(599) PflM I(646) ApaB I(748) Sca I(4538) Pvu I(4428) Pst I(4303) Bsa I(4119) Eam1105 I(4058) Ap ( ) pet-21a(+) (5443bp) laci ( ) Mlu I(1064) Bcl I(1078) BstE II(1245) Bmg I(1273) Apa I(1275) BssHII(1475) EcoR V(1514) Hpa I(1570) AlwN I(3581) ori (3227) PshA I(1909) BspLU11 I(3165) Sap I(3049) Bst1107 I(2936) Tth111 I(2910) BspG I(2691) PpuM I(2171) Psp5 II(2171) Bpu10 I(2271) pet21 - novagen.com

22 Promotor Structure - Plasmid T7 promoter primer # Bgl II T7 promoter lac operator Xba I rbs Eag I Nde I Nhe I Ava I T7 Tag BamH I EcoR I Sac I Sal I Hind III Not I Xho I His Tag Nco I Bpu1102 I T7 terminator T7 terminator primer # pet3 - novagen.com

23 Translation Tools