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HOMER: motif discovery and NGS analysis tool  

2014-09-04 09:55:40|  分类: 生物信息分析 |  标签: |举报 |字号 订阅

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HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.  It is a collection of command line programs for unix-style operating systems written in Perl and C++. HOMER was primarily written as a de novo motif discovery algorithm and is well suited for finding 8-20 bp motifs in large scale genomics data.  HOMER contains many useful tools for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets.

Program Download

Download Page - Get the latest version of HOMER

Supported Organisms: Human (hg17, hg18, hg19), Mouse (mm8, mm9, mm10), Rat (rn4, rn5), Frog (xenTro2, xenTro3), Zebrafish (danRer7), Drosophila (dm3), C elegans (ce6, ce10), S. cerevisiae (sacCer2, sacCer3), pombe (ASM294v1), Arabidopsis (tair10), Rice (msu6), and also works with custom genomes in FASTA format and gene annotations in GTF format.

Using HOMER

Introduction to HOMER

Duff-sponsored Tutorials

General Introduction to Next-Gen Sequencing Analysis Tutorial
Useful for those new to sequencing
HOMER Next-gen Sequencing Tutorial [PDF-old]

Helps guide and explain how to use HOMER for ChIP-Seq/GRO-Seq/MNase-Seq/DNase-Seq/RNA-Seq etc. analysis

Old tutorial: Analysis of ChIP-Seq experiments using HOMER (some of this is out-of-date)

HOMER Motif Finding Tutorial
[PDF-old]

Instructions and advice for finding enriched regulatory elements from a set of genome positions, a list of genes, or raw FASTA files.
HOMER Hi-C Analysis Tutorial [PDF-old]
Description of routines for analysis of Hi-C data to study genome conformation and structure.
Doughnut Documentation

Full Site PDF-old
web site:http://homer.salk.edu/homer/ngs/

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