尝试做细菌完成图的你是不是有很多疑问 这份避坑指南请收好! 答:“1 Contig,0 Gap”的承诺保证了组装的完整性。但细菌基因组也存在多条染色体的现象,染色体本身又分线性和环状两种情况,受限于细菌本身客观情况的需要具体调整。凌恩生物超过几百个完成图的项目经验,多种微生物包含多个环、多个质粒,我们承诺都可以完成。。。 答:需要提供菌的拉丁名给公司进行确认,传染性太高的菌可能无法承接。 答:五个工作日。 答:基因预测(gene、CDS、tRNA、rRNA、23S rRNA 、16S rRNA、5S rRNA 、miscRNA、tmRNA);假基因预测;CRISPR 序列预测;基因岛预测;前噬菌体预测;重复序列预测;次级代谢基因簇预测。 答:标准分析通用数据库(Nr、KEGG、GO、Swiss-Prot、COG、CARD、CAZy)及专有数据库(VFDB、PHI、Antismash、TCDB、ARDB、Pfam、CYP450)。 答:DNA样品澄清透明,总量≥2 μg; 答:提供单菌菌体样本。 1、不建议送平板和带液体培养基的,如有需求,请提前和实验室沟通。 答:除以下情况之外,可以保证达到完成图水平,我们承诺100%项目获得完成图。 a. 基因组大小>7M;基因组大小不限,最大基因组完成图14mb链霉菌; b. 样品不纯(包括但不限于其它物种序列污染);污染比例低于5%都可以承诺; c. 染色体基因组个数+质粒个数>4; d. 转座子或其它重复序列在基因组中的比例异常高(>10%); e. 最长重复序列大于9K; f. GC比例低于30%或高于70%。 以上情况特殊的项目,本公司项目经验丰富均可承接,并承诺组装做到最好。 答:由于HiFi数据兼具长读长和高质量的特性,在基因组组装中无需纠错,可实现基因组的快速组装,让基因组组装进入“高铁”时代。 答:可以的,细菌完成图与细菌甲基化的实验流程是一致的,可以共用一份数据。要求数据量更高,推荐300x以上的覆盖度。 答:可以的。我们承诺组装得到该菌株的全部质粒基因组。
如下图,沙门与大肠就属于种间关系,K-12和857C属于种内关系,其都属于大肠杆菌。 种内污染:相同物种、不同菌株混合在一起的样品,即下图中K-12与857C两个大肠菌株没有分离成功,而混合在一起抽提DNA,进行后续基因组组装的过程。 我们以三种常见的细菌作为测试对象:
(1)从基因组大小来看,种间还是影响更大(非常容易理解,污染了其他物种基因组,组装结果中拥有污染物种序列,明显会增大); 总结:种间污染不可怕,除了组装大小偏大,其他影响较小,而且可以通过生物信息方法排除污染,改善组装质量;但是种内污染比较麻烦,不容易排除污染,会让人束手无策,无法改善结果。 特别提示: 公司完成图 (部分文章列表) 9. Comparative genomic analysis of iprodione-degradingPaenarthrobacter strains reveals the iprodione catabolic molecular mechanism inPaenarthrobacter sp. strain YJN-5. Environmental Microbiology, 2020.(IF=4.933) 10. A novel strain of acetic acid bacteria Gluconobacteroxydans FBFS97 involved in ribofavin production. Scientific Reports, 2020.(IF=3.998) 11. An angular dioxygenase gene cluster responsible forthe initial phenazine-1-carboxylic acid degradation step in Rhodococcus sp.WH99 can protect sensitive organisms from toxicity. Science of the TotalEnvironment, 2020. (IF=5.589) 12. Novel Black Yeast-like Species in Chaetothyrialeswith Ant-associated Life Styles. Fungal Biology, 2020. (IF=2.789) 13. Assembly and analysis of the whole genome ofArthroderma uncinatum strain T10, compared with Microsporum canis and Trichophytonrubrum. Mycoses, 2020. (IF=3.065) 14.. Characterization of a Linezolid- andVancomycin-Resistant Streptococcus suis Isolate That Harbors optrA and vanGOperons. Frontier in Microbiology, 2019. (IF=4.259) 15. Population Structure and Antimicrobial ResistanceTraits of Avian-origin mcr-1-positive Escherichia coli in Eastern China, 2015to 2017. Transboundary and Emerging Diseases, 2019. (IF=3.554) 16. Emergence of plasmid-mediated oxazolidinoneresistance gene poxtA from CC17 Enterococcus faecium of pig origin. Journal ofAntimicrobial Chemotherapy, 2019. (IF=5.113) 17. Genome mining and metabolic profiling illuminate thechemistry driving diverse biological activities of Bacillus siamensis SCSIO05746. Applied Microbiology and Biotechnology, 2019. (IF=3.670) 18. Circulation and Genetic Diversity of FelineCoronavirus Type I and II From Clinically Healthy and FIP-Suspected Cats inChina. Transboundary and Emerging Diseases, 2019. (IF=3.554) 19. Comparative genome analysis reveals the evolutionof chloroacetanilide herbicide mineralization in Sphingomonas wittichii DC‑6.Archives of Microbiology, 2019. (IF=1.642) 20. Relationship between tetracycline antibiotic susceptibility and genotype in oralcavity Lac clinical isolates. Antimicrobial resistance and infection control,2019. (IF=3.568) 21. Complete Genome Sequence of Cd(II)-ResistantArthrobacter sp. PGP41, a Plant Growth-Promoting Bacteriumwith Potential in Microbe-Assisted Phytoremediation. Current Microbiology, 2018.(IF=1.373) 22. Characterization and heterologous expressionof the neoabyssomicin/abyssomicin biosynthetic gene cluster from Streptomyces koyangensisSCSIO 5802. Microbial Cell Factories, 2018. (IF=3.831) 23 Phylogeny of dermatophytes with genomic characterevaluation of clinically distinct Trichophyton rubrum and T.violaceum. Studies in mycology, 2018. (IF=11.663) 24. Genome Sequencing of Streptomyces atratus SCSIOZH16and Activation Production of Nocardamine via Metabolic Engineering. Frontier inMicrobiology, 2018. (IF=4.076) 25. Biodegradation of di-n-butyl phthalate (DBP) by anovel endophytic Bacillus megaterium strain YJB3. Science of the TotalEnvironment , 2017. (IF=4.610) 26. Deciphering the sugar biosynthetic pathway andtailoring steps of nucleoside antibiotic A201A unveils a GDP-L-galactose mutase.PNAS, 2017. (IF=9.423) 27. Biosynthesis of ilamycins featuring unusualbuilding blocks and engineered production of enhanced anti-tuberculosis agents.Nature Communications, 2017. (IF=12.353) 28. The complete genome sequence of Bacillus velezensis9912D reveals its biocontrol mechanism as a novel commercial biologicalfungicide agent. Journal of Biotechnology, 2017. (IF=2.533) |
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