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celia2012铜虫 (小有名气)
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[求助]
有谁能帮我大致翻译一下英文文献中一个实验方法：是关于分子生物学的内容
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有谁能帮我大致翻译一下英文文献中一个实验方法：是关于分子生物学的内容,真心搞不懂啊.拜托分子生物专业人士了~ 2.6. High-throughput sequencing of environmental metagenome High-throughput sequencing of the drinking water metagenome was performed in Beijing Genome Institute (Shenzhen,China) by using Illumina Hiseq 2000. The sequencing strategy of Index 101 PE (Paired-End sequencing, 101-bp reads and 8-bp index sequence) was applied to generate nearly equal amount of clean reads for each sample. The raw reads containing three or more “N” or contaminated by adapter (>15 bp overlap) were removed, and the filtered clean reads (about 1.6 Gb per each sample) were used for metagenomic analyses (Table S4). The metagenomic data have been deposited in NCBI Sequence Read Archive under accession number SRA050945. 2.7. Bioinformatic analysis on high-throughput sequencing All the clean reads were assembled de novo by using SOAPdenovo (BGI, Shenzhen, China) with optimal Kmer at 43 (FW),45 (DW) and 47 (TW) to generate contigs. The detailed information about the sequencing reads and assembling results was described in Tables S4 and S5. Both the nucleotide and protein database of ARGs were established by downloading the sequences in the MvirDB which collected all publicly available organized sequences (5642 sequences of both nucleotide and protein) of ARGs (Zhou et al., 2007). A read was annotated as ARG according to its best BLAST hit (BLASTn or BLASTx with the E-value cut-off at 105) if (1) the similarity was above 90% and (2) the alignments had at least 50 bp (for nucleotide database) or 25 amino acids (for protein database) (Kristiansson et al., 2011). The nucleotide sequences of MGEs including integrons,insertion sequences and plasmids were downloaded from INTEGRALL (1447 integrase genes and 8053 gene cassettes) (Moura et al., 2009), ISfinder (2578 sequences, 22 families of insertion sequences) (Siguier et al., 2006) and NCBI RefSeq database (2408 plasmid genome sequences), respectively. A read was identified as integron or insertion sequence if the BLAST hit (BLASTn with the E-value cut-off at 105) had a sequence identity of more than 90% over an alignment of at least 50 bp (Kristiansson et al., 2011). The threshold of identified plasmids was determined as the BLAST hits (BLASTn with the E-value cut-off at 105) with a nucleotide sequence identity of above 95% over an alignment of at least 90 bp(Kristiansson et al., 2011).Based on the assembled contigs (Table S5), open reading frames (ORFs) were predicted by using MetaGeneMark, and amino acid sequences of the putative ORFs were compared against the NCBI non-redundant protein database to generate results (format 0). MEGAN 4 software (Huson et al.,2011) was used to assign BLAST results to NCBI taxonomies with the Lowest Common Ancestor algorithm using default parameters (absolute cutoff: BLAST bitscore 35; relative cutoff: 10% of the top hits). The relative abundance of each classification was calculated by normalizing the assigned sequences to the total number of ORFs  |
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zhang881007
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celia2012: 金币+4, ★★★很有帮助 2013-01-10 18:46:34
感谢参与，应助指数 +1
celia2012: 金币+4, ★★★很有帮助 2013-01-10 18:46:34
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几个关键点。其他你自己能看就行，我不翻了 Illumina Hiseq 2000（是测序用的设备） 数据的去留方法为：原始读取含有三个或更多的“N”或者适配器（> 15 bp的重叠）除去，数据已经存放在NCBI序列读取压缩文件加入数SRA050945下。 数据信息分析 按 Zhou等，2007和KRISTIANSSON等人，2011方法进行。 最后是简述信息分析中的优化方法。 这些都是程序预设的参数出处。如果你要详细翻译，建议找个翻译软件把。 |
2楼2013-01-10 11:16:00
