Riba:
- Ikon buga lambar mahimman ayyukan bincike na jeri kamar karatun FASTA, fassarar, daidaitawa da BLAST da fassara sakamakon.
- Ikon guje wa yanke shawara mara kyau ta hanyar fassara daidaitattun ra'ayoyi kamar e-daraja, ƙimar ɗaukar hoto da firam ɗin karatu.
- Ikon fahimtar wajibcin tabbatar da da'awar aikin jeri tare da bayanan hukuma (NCBI, UniProt, Ensembl).
Mafi mahimman bayanai na ilimin halitta shine jerin: jerin DNA wanda ya ƙunshi haruffa A, T, G, C; A, U, G, C jerin RNA; sarkar amino acid haruffa 20 na furotin. Mun fahimci menene kwayar halitta, yadda nau'ikan nau'ikan biyu ke da alaƙa, da alaƙar maye gurbi (canji a jere) da cuta ta waɗannan jeri. A cikin wannan rukunin, za mu koyi yin amfani da hankali na wucin gadi azaman lamba da mataimaki na fassara don nazarin jeri: karanta fayilolin FASTA, fassarar jeri, daidaitawa (daidaitawa: kwatanta haruffa biyu ta wasiƙa da ganin kamancensu), da fahimtar kayan aikin kamar BLAST.
Mahimmin faɗakarwa daga farkon: AI bai "san" ainihin aikin jeri ba; Saitunan bayanai na hukuma (NCBI, UniProt, Ensembl) da hujjoji masu ƙarfi sun faɗi wannan.
Basic Concepts da kayan aiki
- FASTA: Tsarin rubutu wanda ke adana kirtani; Kowace tsararru ta ƙunshi layin kai da ke farawa da> da layin ƙasa da ke ƙasansa.
- BLAST (Tsarin Kayan Aikin Neman Daidaita Gida): Kayan aiki ne wanda ke kwatanta jerin da kuke da shi tare da miliyoyin jeri a cikin babban ma'ajin bayanai kuma ya sami mafi kamanceceniya. "Me wannan silsilar yayi kama?" daidaitaccen amsar tambayar.
- Daidaitawa: Shirya jeri biyu ko fiye don a sanya yankuna iri ɗaya a ƙarƙashin ɗayan. Yana iya zama hanya biyu ko daidaita jeri da yawa (MSA).
- Fassara: Maida jerin lambobin DNA/RNA zuwa jerin amino acid ta rukunin haruffa uku (codons).
- Motif: taƙaitaccen tsari mai maimaitawa a cikin jeri wanda ke da ma'anar aiki (misali, wurin ɗaure).
Tukwici: Ba za ku iya gaya wa AI don "BLAST waccan jerin" ba; Samfurin ba zai iya samun dama ga bayanan BLAST ba. Amma "Ta yaya zan fassara sakamakon BLAST na, menene ma'anar e-daraja (E-darajar)?" Kuna iya tambaya, har ma da rubuta lambar da ke kiran BLAST da tsari tare da Biopython.
Mataki-mataki: bincika ainihin tsararru
- Samu jerin: Ajiye don fayil azaman FASTA.
- Binciken asali: Tsawon tsayi, abun ciki na harafi (kawai A/T/G/C ne ko kuma akwai “N” da ba a sani ba), rabon GC (kashi na guanine-cytosine: ya bambanta ta jinsi da yanki).
- BLAST: Bincika a cikin mahaɗin yanar gizo na NCBI ko ta hanyar shirye-shirye.
- Sharhi: Dubi e-darajar mafi kyawun wasa (ƙaramin shi, ƙarancin yuwuwar zama daidaituwa) da ɗaukar hoto.
- Tabbatarwa: Buɗe kwayar halitta/protein da ta dace a cikin UniProt ko NCBI kuma tabbatar da cewa ya yi daidai da aikin da kuke nema.
AI yana taimaka muku lamba a mataki na 2 da yin sharhi a mataki na 4; amma ainihin bayanai a cikin matakai na 3 da 5 an samar da su ta kayan aikin kansu da ku.
Samfuran gaggawar da za a iya kwafi
Matsayi: Kai mataimakin bioinformatics ne. Aiki: Karanta fayil ɗin FASTA (sequences.fasta) tare da Biopython. Ina so: rubuta sunan, tsayi da rabon GC na kowane jeri a cikin tebur; ajiye sakamakon a matsayin CSV. Ba da lambar Python aiki tare da sharhi.
Fassara jerin DNA da nake da su zuwa jerin furotin. Yi amfani da Biopython Seq.fassara; nuna tasha codon (*); nuna firam ɗin karatu. Ba da lamba, bayyana.Jeri: [FASTA]
Fassara sakamakon BLAST na. A ƙasa akwai ƙima-daraja, adadin ainihi, da ƙimar ɗaukar hoto na manyan matches 5. Bayyana mani wane wasa ne abin dogaro kuma me yasa, kar a yi da'awar aiki daidai, gaya mani matakan da nake buƙatar tabbatarwa. Table: [bayanai]
Daidaita jerin sunadaran sunadaran biyu bibiyu kuma sami kamancen kashi. Yi amfani da Biopython pairwise2 ko Bio.Aalign; buga jeri a karanta. Ba da lambar kuma bayyana tsarin ƙira.
Rauni mai ƙarfi / Ƙarfi mai ƙarfi
Rarrauna: "Wane jinsin wannan jeri?"
Mai ƙarfi: "Ina da jerin DNA na ɗan adam na nau'i-nau'i na tushe na 1,140 (FASTA a ƙasa). Na ɓata wannan jerin da kaina; mafi kyawun wasa shine TP53, e-darajar 0.0, ainihi 99.8%, ɗaukar hoto 100% Bayyana dalilin da yasa wannan sakamakon ya zama shaida mai ƙarfi; duk da haka, gaya mani wane tabbaci na 2 da nake buƙatar yin aiki kafin a tabbatar. "
Bambanci: A cikin hanzari mai ƙarfi, ainihin bayanan (tsawon tsayi, sakamakon BLAST) an ba da samfurin; Kuna tambayar samfurin don fassara shaidar da kuka bayar, ba don "tunawa" ba. An tilasta masa ya zama abin ƙira a kan rashin ƙarfi.
uku mini lokuta
Case 1 - Tsarin karatun da ba daidai ba: Wani ɗalibi ya fassara jerin DNA zuwa furotin, amma daga farkon, ba tare da gano ainihin codon farawa ba (ATG). Sakamakon ya kasance mara ma'ana, furotin da ke dakatarwa da wuri. Lokacin da samfurin ya gwada duk firam ɗin karantawa guda uku kuma ya rubuta lambar da ta samo firam ɗin buɗewa mafi tsayi (ORF) wanda ya fara da ATG, daidaitaccen furotin amino acid 380 ya fito.
Case 2 - Fassara E-daraja: Wani masanin fasaha ya ba da rahoton wasan BLAST tare da e-darajar 2.0 a matsayin "an samu". Alhali, e-darajar da ta fi 1 tana nuna cewa wasan ya fi dacewa da daidaituwa. Samfurin ya bayyana wannan kuma ya tunatar da cewa e <1e-5 ana amfani da shi gabaɗaya azaman abin dogaro.
Hali na 3 - Gurɓatawa: BLAST na jerin kwayoyin cuta a cikin dakin gwaje-gwaje ya zama DNA na ɗan adam a matsayin mafi kyawun wasa. Wannan alama ce ta gurɓataccen samfur. AI ta tayar da zato mai kyau ta hanyar bayyana cewa "nau'in wasan da ba zato ba tsammani zai iya zama alamar kamuwa da cuta"; Mai fasaha ya maimaita misalin.
Kwatanta: rawar da basirar wucin gadi
nema
basirar wucin gadi
Kayan aiki/babban bayanai
mutum
FASTA karanta, GC/tsawon
rubuta code
-
Yana sarrafa fitarwa
Fassara, gano ORF
rubuta code
Yana gudanar da Biopython
Yana tabbatar da firam
tsarar id
Sharhi
BLAST/NCBI ya samo
ya tabbatar
Da'awar aiki
yana ba da shawarwari
UniProt yana ba da hujja
yanke shawara
Kuskuren gama gari
- Neman ƙirar don "tuna" ID ɗin kirtani: Samfurin ba ya haddace kirtani; Yi amfani da BLAST.
- Ƙimar e-daraja ta kuskure: Ƙananan yana da kyau, babba ba shi da kyau; Tuna bakin kofa.
- Rashin duba firam ɗin karatu: Firam ɗin da ba daidai ba yana haifar da sunadarin banza.
- Yin watsi da ɗaukar hoto: Babban ainihi amma ƙarancin ɗaukar hoto yana nufin wasa mai ban sha'awa.
- Rashin gurɓataccen abu: Daidaita nau'in nau'ikan da ba a zato ba gargaɗi ne mai tsanani.
Tsanaki: Domin kawai jerin suna "99% kama da TP53" baya tabbatar da cewa jerin yana ɗaukar aikin TP53; Hasashe ne mai ƙarfi. Dole ne a goyi bayan aikin ta tabbatacciyar shaida da kwatancen bayanai. Bai isa ba don AI kawai ya ce "wannan mai hana ƙari ne."
Matsakaicin jeri da yawa da tushen phylogeny
Daidaita jerin jeri da yawa tare maimakon biyu kawai ana kiran su da yawa jerin alignment (MSA) kuma shine ginshiƙi na nazari da yawa: gano yankuna da aka kiyaye (ɓangarorin da ba su canza ba a cikin juyin halitta kuma saboda haka aiki mai mahimmanci), gina bishiyoyin phylogenetic, gano dangin furotin. Kayan aiki kamar MAFFT, MUSCLE da Clustal suna yin wannan aikin. AI yana rubuta lambar da ke kiran waɗannan kayan aikin daga Python (ta hanyar Biopython, alal misali) kuma yana taimaka muku fassara fitarwa; amma alignment kanta yana yin kayan aiki, ba samfurin "by rote".
Lokacin fassara MSA, kula da ginshiƙan da aka adana: amino acid wanda ya kasance iri ɗaya a duk jerin yana da mahimmanci ga aikin furotin (misali, wurin aiki na enzyme). Wannan yana ba da haske mai ƙarfi akan dalilin da yasa maye gurbi zai iya zama cutarwa. Amma "tsare = mahimmanci" hasashe ne; yana buƙatar tabbaci na gwaji.
Karanta fayil na daidaitawa da yawa (aligned.fasta), wanda shine fitowar MAFFT, tare da Biopython. Yi lissafin adadin riƙewa don kowane ginshiƙi; Lissafa sama da kashi 90% masu kariya. Bayyana dalilin da yasa waɗannan matsayi na iya zama masu mahimmancin aiki, kar a da'awar takamaiman aiki.
Maye gurbi da bambance-bambancen tarkon fassarar
Lokacin da kuka ga canjin harafi (bambance-bambancen) a cikin zaren, babban tsalle ne a ce yana da "lalata". Yawancin bambance-bambancen suna tsaka tsaki (marasa tasiri). Lokacin fassara tasirin bambance-bambancen, mutum yana buƙatar duba keɓantattun bayanan bayanai (kamar ClinVar) da bayanan mitar yawan jama'a (kamar gnomAD), ba kalmar AI ba. Idan samfurin ya yi iƙirarin cewa bambance-bambancen shine "mai cutarwa," kar a taɓa rubuta wannan a cikin ƙarshen asibiti ko bincike ba tare da tabbatar da shi tare da waɗannan kafofin ba.
Tushen bayanan bayanai don tabbatarwa
Sanin tushe na hukuma don tabbatar da kowane da'awar a cikin jerin binciken shine garkuwarku mafi ƙarfi daga ƙirƙira na bayanan ɗan adam. Mafi yawan amfani da su:
database
ga me
Tabbatacce na al'ada
NCBI GenBank/RefSeq
Jerin DNA/RNA, bayanan kwayoyin halitta
ID na igiya, tsayi
UniProt
Jerin sunadaran da ayyuka
Aiki, adadin amino acid
tarawa
Bayanin genome, wuraren halittar
Gene-chromosome taswira
ClinVar
Muhimmancin asibiti na bambance-bambancen
Pathogenic / yanke shawara
gnomAD
Bambancin mitar a cikin yawan jama'a
bambance-bambancen rare/na kowa
AI na iya ba da shawarar wane daga cikin waɗannan tushe ya kamata ku duba; Amma kuna yin tambaya kuma kuna karanta sakamakon. "Tsarin ya ce wannan shine abin da UniProt ya ce" ba tabbaci ba ne; Tabbatarwa yana buɗe shafin UniProt da kanka.
A takaice
Binciken jeri shine zuciyar bioinformatics; FASTA, BLAST, daidaitawa da fassarar su ne ainihin ayyuka. AI yana rubuta lambar don waɗannan ayyukan kuma yana taimaka muku fassara sakamakon su, amma kayan aikin (BLAST) da ma'ajin bayanai (NCBI, UniProt) suna ba da ainihin gano jerin abubuwa. Daidai fahimtar ra'ayoyi kamar e-daraja, ɗaukar hoto, da firam ɗin karantawa shine mabuɗin don guje wa ƙarshen ƙarshe. Da'awar aiki koyaushe yana buƙatar shaida mai zaman kanta.
Aikin aikace-aikace
Ɗauki jerin samfurin DNA (ko kwayar halitta da kuka zazzage daga NCBI). Shin AI ta ƙididdige tsayi da rabon GC tare da Biopython, sannan ku fassara shi a cikin duk firam ɗin karantawa uku da lambar buga wacce ta sami ORF mafi tsayi. Gudanar da sakamakon. Sannan bincika wannan jerin da kanka a cikin NCBI BLAST kuma sami ƙirar ta fassara ƙimar e-daraja da ƙimar ɗaukar hoto mafi kyawun wasa. Tabbatar da da'awar aikin samfurin a cikin UniProt.
jerin abubuwan dubawa
- [ ] Na duba tsawon da abun ciki na harafi kafin sarrafa kirtani.
- [ ] Na yi amfani da madaidaicin firam ɗin karatu a cikin fassarar.
- [ ] Na gudu BLAST da kaina, ban "tunatar" samfurin ba.
- [ ] Na fassara ƙimar e-daraja da ƙimar ɗaukar hoto daidai.
- [] Na kimanta nau'in nau'in nau'in nau'in nau'in nau'in nau'in nau'in nau'in nau'in nau'in nau'in nau'in nau'in nau'in nau'in nau'in nau'i nau'i nau'i nau'i nau'i nau'i nau'i nau'i nau'i nau'i nau'i nau'i nau'i nau'i nau'i nau'i nau'i nau'i nau'i nau'i nau'i nau'i nau'i nau'i nau'i nau'i nau'i nau'i nau'i nau'i nau'i nau'i)) sun gwada don gurɓata.
- [ ] Na tabbatar da da'awar aikin tare da bayanan hukuma.