DNA / protein sequence analysis 第九組成員：吳宇軒 497541312 侯卜夫 497541283 朱子豪 497541180 王俊偉 497541568.

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Presentation transcript:

DNA / protein sequence analysis 第九組成員：吳宇軒侯卜夫朱子豪王俊偉

EXERCISE 1. DATABASE SEARCHES 指定題目為第三題自選題目為第五題

NO.3 SRS

SRS Library page

Select “EMBL”

Choose “Extended”

after Extended

Division----hum

Sequence Version---200KB

AllText---polya_signal

Search---found 98 entries

NO.5 NCBI

Protein

Limits

human[ORGN]kinase

Search--1161

EXERCISE 2. DATABASE SIMILARITY SEARCHES AND PAIRWISE SEQUENCE ALIGNMENT Database searching ：第九題 Pairwise sequence alignment ：第二題

9. By default, the hits with E-values below should be selected for use in multiple sequence alignment and profile building. Click on the "Run PSI-Blast iteration 2" button. This refreshes the previous query page. Click the "Format!" button to retrieve results. Sequense: MLKYKPLLKISKNCEAAILRASKTRLNTIRAYGSTVPKSKSFEQDSRKRTQSWTALRVGAILAATSSVAY LNWHNGQIDNEPKLDMNKQKISPAEVAKHNKPDDCWVVINGYVYDLTRFLPNHPGGQDVIKFNAGKDVTA IFEPLHAPNVIDKYIAPEKKLGPLQGSMPPELVCPPYAPGETKEDIARKEQLKSLLPPLDNIINLYDFEY LASQTLTKQAWAYYSSGANDEVTHRENHNAYHRIFFKPKILVDVRKVDISTDMLGSHVDVPFYVSATALC KLGNPLEGEKDVARGCGQGVTKVPQMISTLASCSPEEIIEAAPSDKQIQWYQLYVNSDRKITDDLVKNVE KLGVKALFVTVDAPSLGQREKDMKLKFSNTKAGPKAMKKTNVEESQGASRALSKFIDPSLTWKDIEELKK KTKLPIVIKGVQRTEDVIKAAEIGVSGVVLSNHGGRQLDFSRAPIEVLAETMPILEQRNLKDKLEVFVDG GVRRGTDVLKALCLGAKGVGLGRPFLYANSCYGRNGVEKAIEILRDEIEMSMRLLGVTSIAELKPDLLDL STLKARTVGVPNDVLYNEVYEGPTLTEFEDA

1. 輸入序列 2. 選擇 PDB database 3. 選擇 PSI-BLAST 4. BLAST ！

往下捲動選擇 ”Run PSI-Blast iteration 2”

資料顯示為 checked

1.In the NCBI database, retrieve the protein sequences for mouse hypoxanthine phospho ribosyl transferase (HPRT) and the same enzyme from E. coli in FASTA format.

1. 點選 display settings 2. 選擇 FASTA 格式 3. 挑選符合的結果

Mouse HPRT Sequense: >gi|309315|gb|AAA | hprt [Mus musculus] MPTRSPSVVISDDEPGYDLDLFCIPNHYAEDLEKVFIPHGLIMDRTERLARDVMKEMGGHHIVALCVLKG GYKFFADLLDYIKALNRNSDRSIPMTVDFIRLKSYCNDQSTGDIKVIGGDDLSTLTGKNVLIVEDIIDTG KTMQTLLSLVKQYSPKMVKVASLLVKRTSRSVGYRPDFVGFEIPDKFVVGYALDYNEYFRNLNHVCVISE TGKAKYKA

Advanced search 中選擇 organism 後輸入 E. coli 之全名，並加入搜尋

E. coli 之 HPRT

E. coli HPRT Sequense: >gi| |sp|P0A9M2.1|HPRT_ECOLI RecName: Full=Hypoxanthine phosphoribosyltransferase; Short=HPRT MKHTVEVMIPEAEIKARIAELGRQITERYKDSGSDMVLVGLLRGSFMFMADLCREVQVSHEVDFMTASSY GSGMSTTRDVKILKDLDEDIRGKDVLIVEDIIDSGNTLSKVREILSLREPKSLAICTLLDKPSRREVNVP VEFIGFSIPDEFVVGYGIDYAQRYRHLPYIGKVILLDE