分析工具
Basic Local Alignment Search Tool (BLAST) and Conserved Domain Database (CCD) (National
Center for Biotechnology Information [NCBI])
CRISPR identification program
CRISPRfinder (
http://crispr.u-psud.fr/Server/) is a web-based CRISPR identification platform that allows users to upload their own sequences of interest as well as browse genomes annotated directly from the NCBI database (Grissa et al. 2007). CRISPR Recognition Tool (CRT) (
http://www.room220.com/crt/ [Bland et al. 2007]) is available as a command-line tool or plug-in for several commercially available graphical user interface (GUI) bioinformatics platforms (e.g., Geneious9 [Biomatters]). Both programs identify potential CRISPR spacers and repeats, based on a repeat-finding algorithm.
Genome sequence of interest
Quality control software for RNA sequencing data (e.g., FastQC)
RNA folding prediction software (e.g., NUPACK;
http://www.nupack.org/ [Zadeh et al. 2011])
Sequence motif identification program (e.g., WebLogo [Crooks et al. 2004])
Short read sequence alignment tool (e.g., Bowtie 2 [Langmead and Salzberg 2012])
要点:
CRISPR识别软件:基于重复寻找算法,识别CRISPR的间隔和重复。
目标基因序列
RNA测序数据质量控制软件
RNA折叠预测软件
序列功能域识别程序
短序列比对工具