Analysis of TFIIIA Genomic Sequence

1999/8/3


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目錄

Analysis of TFIIIA Genomic Sequence

Contents

Demo 8-1

Make it work on paper first...

Program Chosen: BestFit

Global vs Local Alignments

Global vs Local Alignments

Info Needed

The mRNA Initiation Site

What happened if program Gaps was used?

... 301 AGGCAAACATGAAGAAGCACTTTAACAGATTCCATAACATCAAGATCTGC 350 | || | | | | | || | | | 1 ..............AGATCTATTGAGAAAGGGCCTTACTGTGTGCTGTAA 36 . . . . . 351 GTCTATG.TGTGCCATTTTGAGAACTGTGGCAAAGCATTCAAGAAACACA 399 | ||| ||| | | | | | | |||| | | 37 TTAGATGCTGTTAGTTATCGCACTCCTGTGTGGACCATTGCATCCATCAC 86 ... . . . . . 600 TGCCATCAGGACCTAGCAGTATGTGATGTGTGTAATCGAAAATTCAGGCA 649 | | ||| ||| | | | || | || | ||| 287 TTACTGAAGGCTAAAGCTGCAAGGGACACAGGAAAGGGCTGATTGCCAAT 336 . . . . . 650 CAAAGATTACTTGAGGGATCATCAGAAAACTCACGAAAAAGAGCGAACTG 699 | || | | | || | | | | | | || | 337 CCTTTCAGACATCGCAAAACTTC......CCGATGCATGTGCGATAATGG 380 ... . . . . . 800 TTGTGAGCATGCTGGCTGCGGGAAATGCTTTGCAATGAAAAAAAGCCTAG 849 | || |||| | | || || | | 481 GAGAGAAGGCGCTGCCGGTGGTGTATAAGCGGTAC............... 515 ...

Summary of Statistics

Demo 8-2

Material and Methods

DHFR-undefined-site-1 CTF/CBP-hs| hsp70.5| CCAAT_site_4| NFI.2 || GR-intron-site-3 CAAT_site(1) || GR-intron-site-4 | IE1.2 | || | | | | || AGCTGCAAGGGACACAGGAAAGGGCTGATTGCCAATCCTTTCAGACATCGCAAAACTTCC 301 ---------+---------+---------+---------+---------+---------+ 360 TCGACGTTCCCTGTGTCCTTTCCCGACTAACGGTTAGGAAAGTCTGTAGCGTTTTGAAGG GR-intron-site-2 TATA-box.2 | his3-Tr-TATA | Ad2MLP_US.3 | (TFIID/TBF)-RS | GAL1-TATA| | TATA-box-CS|| | GR-MT-IIA ||| | D3 c-mos_DS1 | TATA|| | | | | ||| | CGATGCATGTGCGATAATGGTTTGTCCTAGAGCTATATAAACAGGCACACATGGCGGCTA 361 ---------+---------+---------+---------+---------+---------+ 420 GCTACGTACACGCTATTACCAAACAGGATCTCGATATATTTGTCCGTGTGTACCGCCGAT PEA3_RS Ets-1_CS| TCF-2-alpha_CS| CP2-gamma-FBG || PTF1-beta-consensus | || | CAGTGGCTTCTACAAGTTCAGAGGAAGCCGAGGGCAGCTTAGTTACTGAAGGAGAGATGG 421 -----*---+---------+---------+---------+---------+---------+ 480 GTCACCGAAGATGTTCAAGTCTCCTTCGGCTCCCGTCGAATCAATGACTTCCTCTCTACC

String Search

A Kind of Hash Coding: A Dinucleotide Is Defined As a “Word”

A Lookup Table to Store the Position of Each Word

Exercise 8-1

Discussion (I): Program

Discussion (II): Parameters

Listed and Predicted Positions of Splicing Junctions

The Effect of Parameters

Alignments Using Computers

Examples

Possible Alignments

Algorithm vs Scoring Matrix

Algorithm

Back Tracing

Scoring Matrix

Summary

作者:楊永正

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