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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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Presentation Transcript
slide1

Lecture 10

DNA Sequence Analysis &

Gene

Identification

Bioinformatics 89

slide2

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

slide3

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

slide4

Function

Command

GCG

SeqWEB

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Default

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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

slide5

What to do next?

The predictions by these programs is just that: a prediction.

NEVER TRUST A COMPUTER!

slide6

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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