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SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive resource for up-to-date quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains and supplementary online services. SILVA provides a manually curated taxon[……] […] 如果给出两个关键词：生物信息、GC，可能很多人的第一反应是“GC含量”(GC-content)或者“CpG岛”(CpG island)吧。这两个星期开始做非编码RNA(Non-coding RNA)预测(对象是Sinorhizobium meliloti,草木樨中华根瘤菌)，接触到一个以前没听说过的新的“GC理论”：GC-skew.查国内文献，几乎找不到对它的详细介绍（也没有对应的中文翻译，skew有“ 歪，偏， 斜”的意思，通过我对这个理论的理解，就把GC-skew翻译为“GC偏移”吧）。这里翻译一篇Nature上的Review，和大家分享一下。 [……] […] mothur > sffinfo(sff=454Reads_archaea.sff, flow=T) Extracting info from 454Reads_archaea.sff … 10000 20000 30000 40000 50000 60000 70000 80000 90000 92115 It took 68 secs to extract 92115. Output File Names: 454Reads_archaea.fasta 454Reads_archaea.qual 454Reads_archaea.flow m[……] […] MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. MetaPhlAn relies on unique clade-specific marker genes identified from 3,000 reference genomes, allowing:
[…] Summary: Pyrosequencing technologies are frequently used for sequencing the 16S ribosomal RNA marker gene for profiling microbial communities. Clustering of the produced reads is an important but time-consuming task. We present Dynamic Seed-based Clustering (DySC), a new tool based on the greedy clu[……] […] |
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