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I-PacBio-Ubude obugcwele obuyi-16S/18S/ITS Amplicon Sequencing
Ipulatifomu ye-Amplicon (16S/18S/ITS) yathuthukiswa ngeminyaka yolwazi ekuhlaziyweni kwephrojekthi yokwehlukahlukana kwamagciwane, equkethe ukuhlaziywa okuyisisekelo okujwayelekile kanye nokuhlaziywa okwenziwe ngezifiso: ukuhlaziywa okuyisisekelo kuhlanganisa okuqukethwe kokuhlaziywa okujwayelekile kocwaningo lwamanje lwamagciwane, okuqukethwe kokuhlaziywa kucebile futhi kuphelele, futhi imiphumela yokuhlaziya yethulwa ngesimo semibiko yephrojekthi; Okuqukethwe kokuhlaziywa okwenziwe ngezifiso kuyahlukahluka. Amasampula angakhethwa futhi amapharamitha angasethwa ngokuguquguqukayo ngokuya ngombiko wokuhlaziya oyisisekelo kanye nenhloso yocwaningo, ukuze kufezwe izidingo ezenziwe ngezifiso. Uhlelo lokusebenza lwe-Windows, olulula futhi olusheshayo.
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I-Transcriptome Egcwele ye-PacBio (Ayibhekiseli)
Uma sithatha idatha yokulandelelana kwe-Pacific Biosciences (PacBio) Isoform njengokufaka, lolu hlelo lokusebenza luyakwazi ukuhlonza ukulandelana kombhalo ogcwele ubude (ngaphandle kokuhlanganiswa). Ngokuhlela ukulandelana kombhalo ogcwele ubude ngokumelene ne-genome yokubhekisela, imibhalo ingenziwa ngcono yizakhi zofuzo ezaziwayo, imibhalo ebhaliwe, izifunda zokubhala ikhodi, njll. Kulesi simo, ukuhlonza okunembile kakhulu kwezakhiwo ze-mRNA, njengokuhlanganisa okuhlukile, njll., kungafinyelelwa. Ukuhlaziywa okuhlangene nedatha yokulandelelana kwe-NGS transcriptome kwenza kube lula ukuchaza okubanzi kanye nokulinganisa okunembile kakhulu ekuvezeni ezingeni lokubhala, okuzuzisa kakhulu ukuvezwa kokwehluka okungezansi kanye nokuhlaziywa kokusebenza.
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Ama-Toolkit
I-BMKCloud iyipulatifomu ehamba phambili ye-bioinformatic enikeza ikhambi elilodwa lezinhlelo ze-genomic, elithenjwa kakhulu ngabacwaningi ezindaweni ezahlukene okuhlanganisa ezokwelapha, ezolimo, ezemvelo, njll. I-BMKCloud izibophezele ekuhlinzekeni ngezinsizakalo ezihlanganisiwe, ezithembekile nezisebenzayo okuhlanganisa amapulatifomu namathuluzi okuhlaziya i-bioinformatic, izinsiza zokubala, isizindalwazi somphakathi, izifundo eziku-inthanethi ze-bioinformatic, njll. I-BMKCloud inamathuluzi ahlukahlukene asetshenziswa njalo e-bioinformatic okuhlanganisa isichasiselo sezakhi zofuzo, amathuluzi okuguqula izakhi zofuzo, i-ncRNA, ukulawulwa kwekhwalithi yedatha, ukuhlanganiswa, ukuqondanisa, ukukhishwa kwedatha, ukuguqulwa kwezakhi zofuzo, izibalo, umenzi wezibalo, ukuhlaziywa kokulandelana, njll.
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I-RNA Encane
Ama-RNA amancane awuhlobo lwe-RNA emfushane engabhalisi ikhodi enobude obumaphakathi obungu-18-30 nt, kufaka phakathi i-miRNA, i-siRNA kanye ne-piRNA. Lawa ma-RNA amancane kubikwe kakhulu ukuthi ahilelekile ezinqubweni ezahlukahlukene zebhayoloji njengokuchithwa kwe-mRNA, ukuvinjelwa kokuhumusha, ukwakheka kwe-heterochromatin, njll. Ukuhlaziywa kokulandelana kwe-SmallRNA kusetshenziswe kabanzi ezifundweni zokuthuthukiswa kwezilwane/izitshalo, izifo, igciwane, njll. Ipulatifomu yokuhlaziya ukulandelelana kwe-Small RNA iqukethe ukuhlaziywa okujwayelekile kanye nokumbiwa kwedatha okuthuthukisiwe. Ngokusekelwe kwedatha ye-RNA-seq, ukuhlaziywa okujwayelekile kungafeza ukuhlonza nokubikezela kwe-miRNA, ukubikezela kwe-gene target ye-miRNA, ukuhlaziywa kokuchazwa kanye nokubonakaliswa. Ukuhlaziywa okuthuthukisiwe kuvumela ukusesha kanye nokukhipha kwe-miRNA okwenziwe ngokwezifiso, ukukhiqizwa kwedayagramu ye-Venn, i-miRNA kanye nokwakhiwa kwenethiwekhi yegene target.
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I-NGS-WGS (Illumina/BGI)
I-NGS-WGS iyipulatifomu yokuhlaziya kabusha i-genome, eyakhiwa ngokusekelwe kokuhlangenwe nakho okucebile ku-Biomarker Technologies. Le pulatifomu elula ukuyisebenzisa ivumela ukuhanjiswa okusheshayo komsebenzi wokuhlaziya ohlanganisiwe ngokumane usethe ipharamitha embalwa eyisisekelo, efanela idatha yokulandelela i-DNA ekhiqizwe kusuka kokubili ipulatifomu ye-Illumina kanye nepulatifomu yokulandelela i-BGI. Le pulatifomu isetshenziswa kuseva yekhompyutha esebenza kahle kakhulu, enika amandla ukuhlaziywa kwedatha okuphumelelayo kakhulu ngesikhathi esilinganiselwe kakhulu. Ukumbiwa kwedatha yomuntu siqu kuyatholakala ngokusekelwe ekuhlaziyweni okujwayelekile, kufaka phakathi umbuzo wezakhi zofuzo oguquliwe, ukwakheka kwe-primer ye-PCR, njll.
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i-mRNA (Ireferensi)
I-Transcriptome iyisixhumanisi phakathi kolwazi lwezakhi zofuzo lwe-genomic kanye ne-proteome yomsebenzi wezinto eziphilayo. Ukulawulwa kwezinga lokuloba kuyindlela yokulawula yezinto eziphilayo ebaluleke kakhulu futhi efundwa kabanzi. Ukulandelana kwe-transcriptome kungalandelanisa i-transcriptome nganoma yisiphi isikhathi noma ngaphansi kwanoma yisiphi isimo, ngesinqumo esinembile ku-nucleotide eyodwa. Ingabonisa ngokuguquguqukayo izinga lokubhalwa kwezakhi zofuzo, ihlonze futhi ilinganise imibhalo engavamile nejwayelekile ngasikhathi sinye, futhi inikeze ulwazi lwesakhiwo semibhalo ethile yesampula.
Njengamanje, ubuchwepheshe bokulandelana kwe-transcriptome busetshenziswe kabanzi kwezolimo, kwezokwelapha nakweminye imikhakha yocwaningo, okuhlanganisa nokulawulwa kokuthuthukiswa kwezilwane nezitshalo, ukuzivumelanisa nemvelo, ukusebenzisana kwamasosha omzimba, indawo yezakhi zofuzo, ukuvela kwezakhi zofuzo zezinhlobo kanye nokutholwa kwesifo sofuzo kanye nezicubu.
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I-Metagenomics (NGS)
Le nkundla yokuhlaziya yenzelwe ukuhlaziywa kwedatha ye-shotgun metagenomic ngokusekelwe eminyakeni yokuhlangenwe nakho. Iqukethe ukuhamba komsebenzi okuhlanganisiwe okuqukethe ukuhlaziywa okuhlukahlukene kwe-metagenomics okudingekayo okuhlanganisa ukucubungula idatha, izifundo zezinga lezinhlobo, izifundo zezinga lomsebenzi wezakhi zofuzo, ukubopha i-metagenome, njll. Ngaphezu kwalokho, amathuluzi okumba idatha enziwe ngokwezifiso ayatholakala ngokuhamba komsebenzi ojwayelekile wokuhlaziya, kufaka phakathi umbuzo wezakhi zofuzo nezinhlobo, ukusetha amapharamitha, ukukhiqiza izibalo ezenziwe ngokwezifiso, njll.
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I-LncRNA
Ama-RNA amade angabhalisi (i-lncRNA) awuhlobo lwemibhalo ebhalwe phansi enobude obungaphezu kwama-200 nt, engakwazi ukubhala amaprotheni. Ubufakazi obuqongelelekayo busikisela ukuthi iningi lama-lncRNA cishe lizosebenza. Ubuchwepheshe bokulandelana okuphezulu kanye namathuluzi okuhlaziya i-bioinformatic asinika amandla okwembula ukulandelana kwe-lncRNA kanye nolwazi lokubeka kahle futhi asiholele ekutholeni ama-lncRNA anemisebenzi ebalulekile yokulawula. I-BMKCloud iyaziqhenya ngokuhlinzeka amakhasimende ethu ngeplatifomu yokuhlaziya ukulandelana kwe-lncRNA ukuze kufezwe ukuhlaziywa kwe-lncRNA okusheshayo, okuthembekile nokuguquguqukayo.
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I-GWAS
Ucwaningo lokuhlobana kwezakhi zofuzo (i-GWAS) luhlose ukuhlonza izinhlobo ezahlukene zezakhi zofuzo (i-genotype) ezihlotshaniswa nezici ezithile (i-phenotype). Izifundo ze-GWA zihlola izimpawu zezakhi zofuzo eziwela i-genome yonke yabantu abaningi futhi zibikezela ukuhlangana kwezakhi zofuzo-i-phenotype ngokuhlaziywa kwezibalo ezingeni labantu. Ukulandelana kabusha kwezakhi zofuzo kungathola cishe zonke izinhlobo zezakhi zofuzo. Uma kuhlanganiswa nedatha ye-phenotypic, i-GWAS ingacutshungulwa ukuze kuhlonzwe ama-SNP ahlobene ne-phenotype, ama-QTL kanye nezakhi zofuzo ezikhethiwe, okusekela kakhulu ukuzalaniswa kwezilwane/izitshalo kwesimanje. I-SLAF isu lokulandelelana kwezakhi zofuzo elenziwe lula, elithola izimpawu ezisakazwa nge-genome, i-SNP. Lawa ma-SNP, njengezimpawu zezakhi zofuzo zama-molecule, angacutshungulwa ukuze kuhlonzwe izici ezihlosiwe. Liyisu elingabizi kakhulu ekuboneni izici eziyinkimbinkimbi ezihambisana nokwehlukahluka kwezakhi zofuzo.
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I-Nanopore i-transcriptomics yobude obugcwele
Ama-isoform ayinkimbinkimbi futhi ahlukahlukene ahlukile ezintweni eziphilayo ayizindlela ezibalulekile zofuzo zokulawula ukuvezwa kwezakhi zofuzo kanye nokuhlukahluka kwamaprotheni. Ukuhlonza ngokunembile izakhiwo zombhalo oqoshiwe kuyisisekelo sokutadisha ngokujulile amaphethini okulawula ukubonakaliswa kwezakhi zofuzo. Ipulatifomu yokulandelana kwe-nanopore iphumelele ukuletha ucwaningo lwe-transcriptomic ezingeni le-isoform. Le pulatifomu yokuhlaziya iklanyelwe ukuhlaziya idatha ye-RNA-Seq ekhiqizwe epulatifomu ye-Nanopore ngokusekelwe ku-genome yokubhekisela, efinyelela ukuhlaziywa kwekhwalithi kanye nokwenani kokubili ezingeni lezakhi zofuzo kanye nezinga lombhalo oqoshiwe.
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i-circ-RNA
I-RNA eyindilinga (i-circRNA) uhlobo lwe-RNA engakhiphi ikhodi, okutholakale muva nje ukuthi idlala indima ebalulekile kumanethiwekhi okulawula ahilelekile ekuthuthukisweni, ukumelana nemvelo, njll. Ihlukile kuma-molecule e-RNA aqondile, isib. i-mRNA, i-lncRNA, iziphetho ze-3′ kanye ne-5′ ze-circRNA zihlanganiswa ndawonye ukuze zakhe isakhiwo esiyindilinga, esizisindisa ekugayweni kwe-exonuclease futhi zizinzile kakhulu kune-RNA eningi eqondile. I-CircRNA itholakale inemisebenzi eyahlukahlukene ekulawuleni ukubonakaliswa kwezakhi zofuzo. I-CircRNA ingasebenza njenge-ceRNA, ebopha i-miRNA ngokuncintisana, eyaziwa ngokuthi i-miRNA sponge. Ipulatifomu yokuhlaziya ukulandelana kwe-CircRNA inika amandla ukuhlaziywa kwesakhiwo se-circRNA kanye nokubonakaliswa, ukubikezela okuqondiwe kanye nokuhlaziywa okuhlangene nezinye izinhlobo zama-molecule e-RNA.
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I-BSA
Ipulatifomu Yokuhlaziya Okuhlukanisiwe Okuhlanganisiwe iqukethe ukuhlaziywa okujwayelekile kwesinyathelo esisodwa kanye nokuhlaziywa okuthuthukisiwe okunezilungiselelo zamapharamitha ezenziwe ngokwezifiso. I-BSA iyindlela esetshenziswa ukuhlonza ngokushesha izimpawu zofuzo ezihlobene ne-phenotype. Ukuhamba komsebenzi okuyinhloko kwe-BSA kuqukethe: 1. ukukhetha amaqembu amabili abantu abanezimpawu zofuzo eziphikisana kakhulu; 2. ukuhlanganisa i-DNA, i-RNA noma i-SLAF-seq (Ethuthukiswe yi-Biomarker) yabo bonke abantu ukuze bakhe inqwaba ezimbili ze-DNA; 3. ukuhlonza ukulandelana okuhlukile ngokumelene ne-genome yokubhekisela noma phakathi, 4. ukubikezela izifunda ezixhunywe yi-candidate nge-algorithm ye-ED kanye ne-SNP-index; 5. Ukuhlaziywa kokusebenza kanye nokucebisa izakhi zofuzo ezifundeni ezikhethiwe, njll. Ukumbiwa kwedatha okuthuthukisiwe okuhlanganisa ukuhlolwa kwezimpawu zofuzo kanye nomklamo we-primer nakho kuyatholakala.
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I-Amplicon (16S/18S/ITS)
Ipulatifomu ye-Amplicon (16S/18S/ITS) yathuthukiswa ngeminyaka yolwazi ekuhlaziyweni kwephrojekthi yokwehlukahlukana kwamagciwane, equkethe ukuhlaziywa okuyisisekelo okujwayelekile kanye nokuhlaziywa okwenziwe ngezifiso: ukuhlaziywa okuyisisekelo kuhlanganisa okuqukethwe kokuhlaziywa okujwayelekile kocwaningo lwamanje lwamagciwane, okuqukethwe kokuhlaziywa kucebile futhi kuphelele, futhi imiphumela yokuhlaziya yethulwa ngesimo semibiko yephrojekthi; Okuqukethwe kokuhlaziywa okwenziwe ngezifiso kuyahlukahluka. Amasampula angakhethwa futhi amapharamitha angasethwa ngokuguquguqukayo ngokuya ngombiko wokuhlaziya oyisisekelo kanye nenhloso yocwaningo, ukuze kufezwe izidingo ezenziwe ngezifiso. Uhlelo lokusebenza lwe-Windows, olulula futhi olusheshayo.
