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http://www.cgl.ucsf.edu/chimera/ UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated. Chimera includes complete documentation and several tutorials, and can be downloaded free of charge for academic, […] 1. 序列分类和种系分析：保守序列直接在GenBank上进行BLAST比较，所有序列使用欧洲生物信息学院的ClustalW2排列，然后用RDPII9.49进行分类。 序列≧98%一致性的定为同一种，用MEGA4.0进行相邻合并分析绘制种系结构图。 2. 统计学分析：使用Graphpad Prism 软件进行配对卡方检验分析。 Starting from a Shell Script In this tutorial we will develop a Bpipe pipeline script for a realistic (but simplified) analysis pipeline used for variant calling on NGS data. In this pipeline the following stages are executed: sequence alignment using bwa sorting and indexing output files using samtools PCR duplicate removal using Picard calling variants […] Summary: Next generation sequencing (NGS) techniques have been widely used to document the small RNAs implicated in a variety of biological, physiological and pathological processes. An integrated computational tool is needed for handling and analyzing the enormous data sets from small RNA deep sequencing approach. Here we present a novel web server, CPSS (A […] MetaVelvet: a short read assember for metagenomics Introduction Motivation: An important step of “metagenomics” analysis is the assembly of multiple genomes from mixed sequence reads of multiple species in a microbial community. Most conventional pipelines employ a single-genome assembler with carefully optimized parameters and post-process the resulting scaffolds to correct assembly errors. Limitations of the […] |
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