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DNA Sequence Analysis & Gene Identification

Lecture 10. DNA Sequence Analysis & Gene Identification. Bioinformatics 89. 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.

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DNA Sequence Analysis & Gene Identification

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  1. Lecture 10 DNA Sequence Analysis & Gene Identification Bioinformatics 89

  2. 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 (AAAAAA)n 3’ 7-mG cap Exon 1 Exon 2 Exon 3 Exon 4 The Organization of an Eukaryotic Gene

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

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

  6. Exercise89-10 Programs used in this exercise: (1) Sequence manipulation – reverse (2)Graphics output – gif (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.

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