核苷酸序列中的基序发现工具Weeder

### 1. conda 安装
 
conda install weeder
 
### 2. 源码安装
# 软件下载，解压
wget http://159.149.160.88/modtools/downloads/weeder2.0.tar.gz
 
mkdir weeder2.0
tar -zxvf weeder2.0.tar.gz -C ./weeder2.0
 
# 编译
cd weeder2.0
 
g++ weeder2.cpp -o weeder2 -O3
 
### 3.运行
weeder2 -f input_file [-O frequency_file_organism_code] [options]
 

input_file must be in Multi-FASTA format.

When no organism code for oligo frequency files is provided it is assumed to be HS (Homo sapiens).

Oligo frequency files for the following organisms are available in the standard Weeder 2.0 package:

Homo sapiens - Code: HS

Mus musculus - Code: MM

Drosophila melanogaster - Code: DM

Saccharomyces cerevisiae - Code: SC

Arabidopsis thaliana - Code: AT

Other frequency files  may be added to the FreqFiles directory by using the "Frequency maker" program

available at http://www.beaconlab.it/modtools

OPTIONS

-chipseq

This flag activates the ChIP-Seq heuristic speeding-up the computation.

-top (DEFAULT: 100)

If the -chipseq parameter is used Weeder 2.0 scans all the input sequences for occurrences of the oligos contained in the top input sequences.

Increase this value when your input has many more than sequences to improve the chance of finding motifs enriched only

in a subset of your input sequences.

-b (DEFAULT: 50)

Weeder 2.0 builds occurrences matrix profiles and outputs (if other conditions are met) only the top scoring motifs

for each motif length. Increase this value to have more (lowest scoring) motifs in the output (see also -maxm).

-maxm (DEFAULT: 25)

To limit the output length, Weeder 2.0 reports only the top scoring motifs with their associated occurrences

matrix and occurrences list. Increase to have longer outputs with more lowest scoring motifs.

-ss

Single strand mode.

ADVANCED OPTIONS

-sim (DEFAULT: 0.95 MIN: 0 MAX: 1)

Similarity threshold for the redundancy filter. This filter removes from the output those motifs that are too similar to other motifs

already reported. Values close to 0 mean a stricter filter and vice versa values close to 1 impose a looser filter.

Set to 1 to disable the filter altogether. Set it to 0 to have in the output only the top scoring oligo for each one of

the possible oligo lengths (6, 8 and 10).

-em (DEFAULT: 1 MIN: 0 MAX: 100)

Weeder 2.0 has a built-in expectation maximization (EM) matrix profiles refinement step.

defines the number of EM cycles to be performed by Weeder 2.0.

One (default) or few EM cycles should be sufficient to "clean" matrix profiles without overfitting them.

参考：

http://159.149.160.88/modtools/