Identification of novel and known miRNAs in deep-sequencing data with miRDeep2 [0.03%]
使用miRDeep2鉴定新的和已知的miRNA
Sebastian D Mackowiak
Sebastian D Mackowiak
miRNAs comprise an abundant class of small non-coding RNAs that play important roles in a wide range of biological processes by post-transcriptional regulation of a large fraction of animal genes. High-throughput sequencing machines and the...
Lincoln D Stein
Lincoln D Stein
Next-generation sequencing (NGS) packs the sequencing throughput of a 2000's-era genome center into a single affordable machine. However, software developed for conventional sequencing technologies is often inadequate to deal with the natur...
Using QIIME to analyze 16S rRNA gene sequences from microbial communities [0.03%]
使用QIIME分析微生物群落的16S rDNA序列
Justin Kuczynski,Jesse Stombaugh,William Anton Walters et al.
Justin Kuczynski et al.
QIIME (canonically pronounced "chime") is a software application that performs microbial community analysis. It is an acronym for Quantitative Insights Into Microbial Ecology, and has been used to analyze and interpret nucleic acid sequence...
Using OrthoMCL to assign proteins to OrthoMCL-DB groups or to cluster proteomes into new ortholog groups [0.03%]
利用OrthoMCL将蛋白划分为OrthoMCL-DB组或将蛋白质组聚类为新的直系同源簇
Steve Fischer,Brian P Brunk,Feng Chen et al.
Steve Fischer et al.
OrthoMCL is an algorithm for grouping proteins into ortholog groups based on their sequence similarity. OrthoMCL-DB is a public database that allows users to browse and view ortholog groups that were pre-computed using the OrthoMCL algorith...
Eukaryotic gene prediction using GeneMark.hmm-E and GeneMark-ES [0.03%]
GeneMark.hmm-E和GeneMark-ES软件包用于真核基因预测
Mark Borodovsky,Alex Lomsadze
Mark Borodovsky
This unit describes how to use the gene-finding programs GeneMark.hmm-E and GeneMark-ES for finding protein-coding genes in the genomic DNA of eukaryotic organisms. These bioinformatics tools have been demonstrated to have state-of-the-art ...
Gene identification in prokaryotic genomes, phages, metagenomes, and EST sequences with GeneMarkS suite [0.03%]
GeneMarkS套装在原核生物基因组、噬菌体、元基因组和EST序列中的基因识别
Mark Borodovsky,Alex Lomsadze
Mark Borodovsky
This unit describes how to use several gene-finding programs from the GeneMark line developed for finding protein-coding ORFs in genomic DNA of prokaryotic species, in genomic DNA of eukaryotic species with intronless genes, in genomes of v...
Michael F Chou,Daniel Schwartz
Michael F Chou
The Web-based motif-x program provides a simple interface to extract statistically significant motifs from large data sets, such as MS/MS post-translational modification data and groups of proteins that share a common biological function. U...
Using the Saccharomyces Genome Database (SGD) for analysis of genomic information [0.03%]
利用Saccharomyces基因组数据库(SGD)分析基因组信息
Marek S Skrzypek,Jodi Hirschman
Marek S Skrzypek
Analysis of genomic data requires access to software tools that place the sequence-derived information in the context of biology. The Saccharomyces Genome Database (SGD) integrates functional information about budding yeast genes and their ...
Jianxing Feng,Tao Liu,Yong Zhang
Jianxing Feng
Model-based Analysis of ChIP-Seq (MACS) is a command-line tool designed by X. Shirley Liu and colleagues to analyze data generated by ChIP-Seq experiments in eukaryotes, especially mammals. MACS can be used to identify transcription factor ...