Bioinformatics Practical for Biochemists Andrei Lupas, Birte Höcker, Steffen Schmidt WS 2013/2014!! 01. DNA Tutorial - notebook / DBs / genome browser / translation
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
Main resources of sequences NCBI (National Center for Biotechnology Information) www.ncbi.nih.gov GenBank as main resource for DNA Common Search Fields [gene] [orgn] [accn] [auth] [titl] EBI (National Center for Biotechnology Information) www.ebi.ac.uk EMBL as main resource for DNA Always record the accession number of your sequence
Dedicated Genome Databases used to be easy now sequencing is cheap personalized genome! http://www.genomesonline.org http://img.jgi.doe.gov
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
Genome Browser The SEED Viewer http://theseed.org/
pubseed.theseed.org
seed-viewer.theseed.org
The SEED: genome information
The SEED: genome information
pubseed.theseed.org
seed-viewer.theseed.org
UCSC Genome Browser http://genome.ucsc.edu
UCSC Genome Browser Get DNA / Screen
UCSC Genome Browser Tracks with annotation information
UCSC Genome Browser
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
AT C G G A T C -18-17 -16-15 -14-13 -12-11 -10-9 -8-7 -6-5 -4-3 -2-1 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 3 4 5 6 7 8 Schneider & Stephens, 1990, NAR
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, http://www.kazusa.or.jp/codon/
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
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 (4977-5432) 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 (3988-4845) pet-21a(+) (5443bp) laci (714-1793) 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
Promotor Structure - Plasmid T7 promoter primer #69348-3 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 #69337-3 pet3 - novagen.com
Translation Tools www.expasy.org http://web.expasy.org/translate/! www.toolkit.tuebingen.mpg.de http://toolkit.tuebingen.mpg.de/sixframe