khai thac ncbi

8/3/2019 khai thac NCBI

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Ti liu chia s ti: wWw.SinhHoc.edu.vn


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Ti liu chia s ti: wWw.SinhHoc.edu.vnS dng Pubmed


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Tm kim trnh t sinh hc 7

Tm kim trnh t sinh hc qua NCBI

Click


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Tm kim trnh t DNA


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Ti liu chia s ti: wWw.SinhHoc.edu.vnTm kim trnh t qua m s truy cp

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M s truy cp ca mt trnh t l m s do cc nh qun trCSDLSH t cho mt trnh t,thng c dng :8 k t: 2 chv 6 s vdnhAY6906406 k t: 1 chv 5 s vdnhU20068


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Ti liu chia s ti: wWw.SinhHoc.edu.vnTM KIM TRNH T SINH HC QUA M S

TRUY CP

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Ti liu chia s ti: wWw.SinhHoc.edu.vnKt qu tm trnh t DNA qua m s truy cp

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Tm kim trnh t qua tn gene


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Ti liu chia s ti: wWw.SinhHoc.edu.vnnh dng FASTA

FASTAl mt gii thut bt cp trnh tcDavid J. Lipman v William R. Pearsonmiu tln u tin vo nm 1985 (Rapid and sensitiveprotein similarity searches).

Nhiuphnmm tin sinh hccnd liu trnht gene hoc protein theo kiu nh dngFASTAnh v d minh hodiy:

>tn trnh tgattctcacttggtctgctgcaaggacgcggaccattaaaactgttcatggcccttgtg

gcgttctcgtttcctaacaatcccaccaacagcagggatactaaaaagatggggaac

gatcaaaaaatcaaaagctatcaatgtcttgagagggttcaggaaagagattggaagat ct aacatctt aaca a ac ca aca ca c t att ttat tt att15
http://vi.wikipedia.org/wiki/B%E1%BA%AFt_c%E1%BA%B7p_tr%C3%ACnh_t%E1%BB%B1http://vi.wikipedia.org/w/index.php?title=David_J._Lipman&action=edit&redlink=1http://vi.wikipedia.org/w/index.php?title=William_R._Pearson&action=edit&redlink=1http://vi.wikipedia.org/wiki/1985http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=2983426http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=2983426http://vi.wikipedia.org/wiki/Ph%E1%BA%A7n_m%E1%BB%81mhttp://vi.wikipedia.org/wiki/Ph%E1%BA%A7n_m%E1%BB%81mhttp://vi.wikipedia.org/wiki/Ph%E1%BA%A7n_m%E1%BB%81mhttp://vi.wikipedia.org/w/index.php?title=Tr%C3%ACnh_t%E1%BB%B1&action=edit&redlink=1http://vi.wikipedia.org/w/index.php?title=Tr%C3%ACnh_t%E1%BB%B1&action=edit&redlink=1http://vi.wikipedia.org/w/index.php?title=Tr%C3%ACnh_t%E1%BB%B1&action=edit&redlink=1http://vi.wikipedia.org/w/index.php?title=Tr%C3%ACnh_t%E1%BB%B1&action=edit&redlink=1http://vi.wikipedia.org/w/index.php?title=Tr%C3%ACnh_t%E1%BB%B1&action=edit&redlink=1http://vi.wikipedia.org/wiki/Ph%E1%BA%A7n_m%E1%BB%81mhttp://vi.wikipedia.org/wiki/Ph%E1%BA%A7n_m%E1%BB%81mhttp://vi.wikipedia.org/wiki/Ph%E1%BA%A7n_m%E1%BB%81mhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=2983426http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=2983426http://vi.wikipedia.org/wiki/1985http://vi.wikipedia.org/w/index.php?title=William_R._Pearson&action=edit&redlink=1http://vi.wikipedia.org/w/index.php?title=David_J._Lipman&action=edit&redlink=1http://vi.wikipedia.org/wiki/B%E1%BA%AFt_c%E1%BA%B7p_tr%C3%ACnh_t%E1%BB%B1


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Ti liu chia s ti: wWw.SinhHoc.edu.vnCch ly trnh t theo nh dng FASTA

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Mt s m s truy cp ca RefSeq database

1. mRNAs and Proteins NM_123456 Curated mRNA

NP_123456 Curated Protein

NR_123456 Curated non-coding RNA

XM_123456 Predicted mRNA XP_123456 Predicted Protein

XR_123456 Predicted non-coding RNA

2. ChromosomeNC_123455 Microbial replicons, organelle

genomes, human chromosomes

4. Assemblies

NT_123456 Contig 17


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Ti liu chia s ti: wWw.SinhHoc.edu.vnV d 1: NM_123456 Curated mRNA

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NM_123456


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Ti liu chia s ti: wWw.SinhHoc.edu.vnV d 2: NC_12345

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S


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Ti liu chia s ti: wWw.SinhHoc.edu.vnKt qu tm kim b gene

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Ti li hi t i W Si hH d


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Blast trnh tSo snh cc chui sinh hc khc nhau(chuiamino-acid, chui DNA), tm kim trnh t tng ng

http://vi.wikipedia.org/w/index.php?title=C%E1%BA%A5u_tr%C3%BAc_ch%C3%ADnh&action=edit&redlink=1http://vi.wikipedia.org/wiki/Amino_acidhttp://vi.wikipedia.org/wiki/Amino_acidhttp://vi.wikipedia.org/w/index.php?title=Chu%E1%BB%97i_DNA&action=edit&redlink=1http://vi.wikipedia.org/w/index.php?title=Chu%E1%BB%97i_DNA&action=edit&redlink=1http://vi.wikipedia.org/wiki/Amino_acidhttp://vi.wikipedia.org/wiki/Amino_acidhttp://vi.wikipedia.org/wiki/Amino_acidhttp://vi.wikipedia.org/w/index.php?title=C%E1%BA%A5u_tr%C3%BAc_ch%C3%ADnh&action=edit&redlink=1


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Ti liu chia s ti: wWw.SinhHoc.edu.vnBLAST thcs l mth cc chng trnh (bao gmcchng trnh blastall). Sau y lmtschng trnh trong h,cspxp theo tht quan trngca n:

Nucleotide-nucleotide BLAST (blastn): khi a vo mt DNA truy vn,strv ccchui DNA gngingnhttcsdliu DNA m ngi dng chnh.

Protein-protein BLAST (blastp): khi a vo mt protein truy vn,strv cc chuiprotein gngingnhttcsdliu protein m ngi dng chnh.

Position-Specific Iterative BLAST (PSI-BLAST): Mt trong nhng chng trnhBLAST mi nht, chng trnh ny dng tm kim cc mi quan h xa ca mtprotein. Trc tin, mt danh sch cc protein lin quan s c to ra. Sau ,nhng protein ny ckthp thnh mt "profile" didngchui trung bnh. Mtcu truy vn timtcsd liu protein sc thc thi nh profile ny, v mtnhm lnhn cc protein c tm thy. Nhm ln ny lic dng to ra mtprofile khc, v qu trnh ny c lp li.

Bng cch thm cc protein lin quan vo vic tm kim, PSI-BLAST tr nn tthntrong vic la ra cc mi quan h tin ha cch xa nhau hn l phn mmchunprotein-protein BLAST.

Nucleotide-protein 6-frame translation (blastx): Chng trnh ny so snh cc snphmchuyni(tru tng) sang 6-khung camtchui nucleotide truy vn(c 2di)vimtcsdliuchui protein. Qu trnh ny c thrtchm.

Nucleotide-nucleotide 6-frame translation (tblastx): Chng trnh ny l chmnht

trong h BLAST. N chuynchui nucleotide truy vn thnh mi 6-khung (frame) cth v so snh cc proteins to thnh. Mc tiu catblastx l tm kimmi quan hrtxa gia cc chui nucleotide.

Protein-nucleotide 6-frame translation (tblastn): Chng trnh ny chuyncsdliuch thnh mi 6-khung (frame) v so snh vichui protein truy vn .

Large numbers of query sequences (megablast): Khi so snh mtslngln ccchuiu vo qua chmt BLAST dng dng lnh, "megablast" l nhanh hnrtnhiuso vichy BLAST nhiuln.

http://vi.wikipedia.org/wiki/Proteinhttp://vi.wikipedia.org/w/index.php?title=M%E1%BB%91i_quan_h%E1%BB%87_ti%E1%BA%BFn_h%C3%B3a&action=edit&redlink=1http://vi.wikipedia.org/w/index.php?title=M%E1%BB%91i_quan_h%E1%BB%87_ti%E1%BA%BFn_h%C3%B3a&action=edit&redlink=1http://vi.wikipedia.org/w/index.php?title=M%E1%BB%91i_quan_h%E1%BB%87_ti%E1%BA%BFn_h%C3%B3a&action=edit&redlink=1http://vi.wikipedia.org/w/index.php?title=M%E1%BB%91i_quan_h%E1%BB%87_ti%E1%BA%BFn_h%C3%B3a&action=edit&redlink=1http://vi.wikipedia.org/w/index.php?title=M%E1%BB%91i_quan_h%E1%BB%87_ti%E1%BA%BFn_h%C3%B3a&action=edit&redlink=1http://vi.wikipedia.org/w/index.php?title=M%E1%BB%91i_quan_h%E1%BB%87_ti%E1%BA%BFn_h%C3%B3a&action=edit&redlink=1http://vi.wikipedia.org/w/index.php?title=M%E1%BB%91i_quan_h%E1%BB%87_ti%E1%BA%BFn_h%C3%B3a&action=edit&redlink=1http://vi.wikipedia.org/w/index.php?title=M%E1%BB%91i_quan_h%E1%BB%87_ti%E1%BA%BFn_h%C3%B3a&action=edit&redlink=1http://vi.wikipedia.org/w/index.php?title=M%E1%BB%91i_quan_h%E1%BB%87_ti%E1%BA%BFn_h%C3%B3a&action=edit&redlink=1http://vi.wikipedia.org/w/index.php?title=M%E1%BB%91i_quan_h%E1%BB%87_ti%E1%BA%BFn_h%C3%B3a&action=edit&redlink=1http://vi.wikipedia.org/w/index.php?title=M%E1%BB%91i_quan_h%E1%BB%87_ti%E1%BA%BFn_h%C3%B3a&action=edit&redlink=1http://vi.wikipedia.org/w/index.php?title=M%E1%BB%91i_quan_h%E1%BB%87_ti%E1%BA%BFn_h%C3%B3a&action=edit&redlink=1http://vi.wikipedia.org/w/index.php?title=M%E1%BB%91i_quan_h%E1%BB%87_ti%E1%BA%BFn_h%C3%B3a&action=edit&redlink=1http://vi.wikipedia.org/w/index.php?title=M%E1%BB%91i_quan_h%E1%BB%87_ti%E1%BA%BFn_h%C3%B3a&action=edit&redlink=1http://vi.wikipedia.org/w/index.php?title=M%E1%BB%91i_quan_h%E1%BB%87_ti%E1%BA%BFn_h%C3%B3a&action=edit&redlink=1http://vi.wikipedia.org/wiki/Protein


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Ti li chia s ti W SinhHoc ed n


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Ti liu chia s ti: wWw SinhHoc edu vn


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Ti liu chia s ti: wWw.SinhHoc.edu.vnSo snh hai trnh t bng blast

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Ti liu chia s ti: wWw SinhHoc edu vnS h H5N1 t t


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Ti liu chia s ti: wWw.SinhHoc.edu.vnSo snh H5N1 v streptococus

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Load trnh t 1

Load trnh t 2

Nhn th



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Ti liu chia s ti: wWw.SinhHoc.edu.vnKt qu bng so snh hai trnh t

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Ti liu chia s ti: wWw.SinhHoc.edu.vnKt qu so snh H5N1 v Streptococus

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Ti liu chia s ti: wWw.SinhHoc.edu.vnPhn tch trnh t DNA: tm khung c m (ORF)



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Thit k primer



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Ti liu chia s ti: wWw SinhHoc edu vnKim tra c hiu mi bng blast


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Ti liu chia s ti: wWw.SinhHoc.edu.vnKim tra c hiu mi bng blast

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Ti liu chia s ti: wWw SinhHoc edu vnN l tid bl t


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Ti liu chia s ti: wWw.SinhHoc.edu.vnNucleotide blast

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Ti liu chia s ti: wWw SinhHoc edu vnNh t h t i


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Ti liu chia s ti: wWw.SinhHoc.edu.vnNhp trnh t mi

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agtggcttgccgctacgactccactgtctgaaaacagccgac

Ti liu chia s ti: wWw SinhHoc edu vnP i bl t


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Ti liu chia s ti: wWw.SinhHoc.edu.vnPrimer blast

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Tnh tng ng ca ca cc primer

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c hiu ca mi

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Ti liu chia s ti: wWw.SinhHoc.edu.vn c hiu ca mi


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Ti liu chia s ti: wWw.SinhHoc.edu.vn c hiu ca mi

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10R1_13785-13806

-Hs Expect: Xc sutca cc trnh t tng

ng. E cng nh chiu cng cao.

- Score v Excpect t lnghch.



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Ti liu chia s ti: wWw.SinhHoc.edu.vnPrimer blast-Chc nng nh gi mi

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Kt qu phn ng nh gi mi

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Ti liu chia s ti: wWw.SinhHoc.edu.vnCch ng k trnh t c gii m qua


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Cch ng k trnh t c gii m quaphn mm sequin

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ChnGenebank

(NCBI)



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Bc 1: in thng tin

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