1 / 7

DNA Sequence Analysis & Gene Identification (I)

Lecture 09. DNA Sequence Analysis & Gene Identification (I). Bioinformatics 90. (AAAAAA)n. 3’. 7-mG cap. Exon 1. Exon 2. Exon 3. Exon 4. The Organization of an Eukaryotic Gene. GENE. Exon 1. Intron. Exon 2. Intron. Exon 3. Intron. Exon 4. Promoter Enhancer.

jaimie
Download Presentation

DNA Sequence Analysis & Gene Identification (I)

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Lecture 09 DNA Sequence Analysis & Gene Identification (I) Bioinformatics 90

  2. (AAAAAA)n 3’ 7-mG cap Exon 1 Exon 2 Exon 3 Exon 4 The Organization of an Eukaryotic Gene GENE Exon 1 Intron Exon 2 Intron Exon 3 Intron Exon 4 Promoter Enhancer Transcription Poly(A) signal mRNA transcript 5’ 3’ 5’-untranslated region Exon 1 Intron Exon 2 Intron Exon 3 Intron Exon 4 3’-untranslated region Processing Mataure mRNA stop start 5’

  3. Gene identification involves 4 main stages Find the putative coding region(s) in the sequence Open reading frame CpG islands Tandemly and dispersed repeats Promoter regions (TATA box, cap signal, CCAAT-box) Transcription factors, Poly-A sites Find non-coding features of interest in the sequence Branch point signal CT(G,A)A(C,T) Determine the exon-intron organization 5’ and 3’ splice sites: AG/GUAAGU--------------PyPyPyPyPyPyPyPy-CAG/G motif, signal and pattern Blast, FASTA Functional studies Identify the gene

  4. GENE FINDERS Banbury Cross http://igs-server.cnrs-mrs.fr/igs/banbury FGENEH http://genomic.sanger.ac.uk/gf/gf.shtml GeneID http://www1.imim.es/geneid.html GeneMachine http://genome.nhgri.nih.gov/genemachine GeneParser http://beagle.colorado.edu/_eesnyder/GeneParser.htl GENSCAN http://genes.mit.edu/GENSCAN.html Genotator http://www.fruitfly.org/_nomi/genotator/ GRAIL http://compbio.ornl.gov/tools/index.shtml GRAIL-EXP http://compbio.ornl.gov/grailexp/ HMMgene http://www.cbs.dtu.dk/services/HMMgene/ MZEF http://www.cshl.org/genefinder PROCRUSTES http://www-hto.usc.edu/software/procrustes RepeatMasker http://ftp.genome.washington.edu/RM/RepeatMasker.html Sputnik http://rast.abajian.com/sputnik/

  5. Function Command GCG SeqWEB + + + + + + + + + + + + + + + + + + + + - - + - Sequence manipulation ORF Searching Mapping (restriction sites) Mapping (transcription factors) Reverse Frames Map Translate Map (-minc) (-maxc) Mapsort (-exclude) (-digest) Mapplot Map tfsites

  6. What to do next? The predictions by these programs is just that: a prediction. NEVER TRUST A COMPUTER!

  7. Exercise89-10 Programs used in this exercise: (1) Sequence manipulation – reverse (3)ORF Searching – frames , map , translate (4)Mapping (restriction sites) – map (-minc, -maxc), mapsort(-exclude, -digest), mapplot, plasmidmap (5)Mapping (transcription factor) – map(tfsites). Sequences used in this exercise: gb:z18853 (C.elegans mRNA for capping protein alpha subunit.) cds:10-858 gb:x03795 (Human mRNA for platelet derived growth factor A-chain, PDGF-A) cds:388-1020.

More Related