Evolutionary Genomics | Akbarjon Rozimov

Bugun sizlarga qanday qilib annotatsiya qilingan fasta fayldan kerak gen qismini alohida ajratib olishni ko'rsataman. Tasavvur qiling 37 ta annotatsiya qilingan gen fasta fayli bor, va aynan sizga faqat COI gene kerak. Buni hech qanday kodsiz shunday copy va paste qilib olish ham mumkin, ammo sizda bir nechta o'nlab yoki yuzlab fasta fayllar bo'lsa bu juda ko'p vaqt saqlash noto'g'ri. Shunday payti python kodlar yodamida xohlagancha fasta fayldan xohlagancha gen qismlarini sekundlar ichida ajratib olishingiz mumkin. Yuqoridagi python skriptda aynan qanday qilib annotatsiya qilingan fasta fayldan COI genni ajratib olib, to'g'ri identifayr yozishni o'rganishingiz mumkin. Va ajratib olingan gen uzunligini seqkit yordamida uzunligini, va head yordamida identifayr to'g'ri yozilganmi ko'rishingiz mumkin. #Extract_gene #Python https://t.me/EvolutionaryGenomics

Shanbani dam olish kuni qiladigan vaqt ham topildi. Va tabiat chiroyidan baxramand bo’ldim. https://t.me/EvolutionaryGenomics

Bugun 13 kun deganda mitochondrial genome assembly qilayotgan 7 ta na’munam tayyor bo’ldi. Input Illumina sekvens juda katta hajmda (40Gb har bir individ) bo’lgani uchun juda ko’p vaqt ketdi. Assembly tugagandan keyingi bosqich annotation. Agar analiz qilayotgan organizmingiz baliq bo’lsa MitoFish onlayn websayti orqali shunchaki assembly fasta faylni yuklash orqali qilish mumkin. Bunda sizga assembly qilingan sekvensni alohida gen bo’laklariga qurib beradi, hamda circular map ham chizadi. Agar baliqdan boshqa tur bo’lsa Mitos2 dasturidan yoki onlayn websaytidan foydalanish mumkin. #Mitogenome #Annotation P.S.: Analiz uchun nuklear genom sekvensidan tashqari mitoxondrial genom konservativ bo’lgani uchun alohida o’rin tutadi. https://t.me/EvolutionaryGenomics

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To whom it may concern, I’m Akbarjon Rozimov, currently pursuing my PhD at the Fish Evolution and Genomics Group, Institute of Zoology, Chinese Academy of Sciences. Akbarjon has been working on evolutionary and conservation genomics of the Shovelnose Sturgeons. The purpose of this channel is to establish first-class genome science community in Uzbekistan, although some posts are written in English, but keep explaining in a simple and human readable way. By sharing fundamental knowledge on molecular structure of life (DNA, RNA, and Proteins), bash scripting (Linux), and design of scientific figures (R & Python), Akbarjon aims to teach you hand-in genomics over pages of textbooks. Keeping an eye on posts, may help you to learn genome assembly, population genomics, adaptive evolution and conservation genomics from scratch and apply these methods and scripts in your scientific research. If you have doubts about any analyses related to above-mentioned, please feel free to contact me: @Akbarjon_Rozimov

To’liq genom sekvensi uchun ishlatiladigan na’munalar -80^C ostidagi muzlatkichda saqlanadi, DNK stabil bo’lsada, RNK lar 20-30 minut ichida RNAaza ta’sirida parchalanish xususiyatiga ega. Shu sabab, -80^C ostida saqlash lozim. P.S.: Chiroq deyarli o’chmaydi, namunalar yillar davomida saqlanib turaveradi. https://t.me/EvolutionaryGenomics

MD5 - 32 ta raqam va harflardan iborat forward/reverse spetsifik kod. MD5 qaysi sekvens bilan ishlayotagnlikni aniq bilishda muhim. @EvolutionaryGenomics

Tepadagi postni yozishimdan asosiy maqsad, ornitologlarga turtki berish. Conservation genomics nuqatayi nazaridan qarasak yovvoyi tabiatdagi va tutqinlikda ko’paytirilgan individlarning genomini tadqiq qilish (inbreeding level (FROH), genetic load, va outbreeding depression) orqali yovvoyi vs. tutqinlikda ko’paytirish orqali tur genetik xilma-xilligi o’zgarish dinamikasini o’rganish mumkin. https://t.me/EvolutionaryGenomics

Yo’rg’a tuvaloq (Chlmydotis macqueenii) O’zbekiston Qizil Kitobiga kiritilgan qush. Ushbu tur har ikkala IUCN Red List va O’zbekiston Qizil Kitobida “Zaif (Vulnerable - VU)” tur bo’lishiga qaramasdan yurtimizda bu qushga bo’lgan e’tibor juda-juda katta. Ekologiya vazirligi “Falcon Hunting Solutions” MChJ bilan birgalikda ushbu qushni tutqinlikda ko’paytirib yovvoyi tabiatga qo’yib yuborish ishlarini bir necha yillardan beri amalga oshirmoqda. Jumladan 2020 yilda Birlashgan Arab Amirliklariga tegishlig bo’lgan Internetnational fund for houbara conservation markazida ko’payitirilgan 2040 bosh yo’rg’a tuvaloq Qoraqalpog’istonning Qo’ng’irot tumanida yovvoyi tabiatga qo’yib yuborilgan. Ekolog.uz ning yozishicha navbatdagi gal 1100 bosh yo’rg’a tuvaloq Navoiy viloyatining Nurota, Navbahor va Konimex tumanlari cho’l hududlariga qo’yib yuborilgan.

The term innovation and intelligence can be here distinguished. Norway recently announced damless turbines that can generate electricity without changing the water flow, affecting fish migration, and blocking water resources for the downstream communities. On the other hand, China is trying to show its power by building a mega dam on the Yarlung-Tsangpo River, called Brahmaputra in Indian section. This dam will be the biggest dam in the world, and biggest project ever done in China. According to reports, the station will generate 300 million megawatt electricity per hour. What will be the consequences if China build this mega dam? 1. India and Bangladesh may suffer serious water shortages nearby the Brahmaputra River areas. 2. The dam will block the migration routes of many endemic fishes, like snow trouts (Schizothorax) and etc. The previous mega dam Three Gorges was costed China to extinction of Chinese Paddlefish (Psephurus gladius) and Yangtze Sturgeon (Acipenser dabryanus).

seqkit stat da yana (-a) flagni qo'llasangiz Q20, Q30, Average Quality, N50, va GC% kontetni ham ko'rsatadi. @EvolutionaryGenomics

Keyingi ajoyib kommand seqkit haqida, seqkit Linux sistemasida sizga sekvens fayllarni strukturasi, sekvens soni, nukleotidlar tarkibi, va boshqa ma'lumotlarni beradi. Atigi seqkit stat XXX.fas ni o'zi yetarli . @EvolutionaryGenomics