【2.2】DNAWorks

一、DNAWorks介绍

官网： https://mcl1.ncifcrf.gov/dnaworks/

• https://hpcwebapps.cit.nih.gov/dnaworks/
• https://github.com/davidhoover/DNAWorks

更多介绍：

• https://wenku.baidu.com/view/9b66d5cff08583d049649b6648d7c1c709a10b7e.html

二、安装

三、使用

使用范例：

/data/software/DNAWorks_ppvm_compile/dnaworks lc_inp.txt

lc_inp.txt：

title "dnaworks"
timelimit 3600
melting low 30 tolerance
frequency threshold 10
concentration oligo 1E-7 sodium 0.05 magnesium 0.002
solutions 2
length low 15 high 60
codon
AAA 0.730
AAC 1.000
AAG 1.000
...

TTT 0.907//
PROTEIN
MEVFLFFLTPGEPASISCRSSQSL//

参数说明，见 https://github.com/davidhoover/DNAWorks

四、报错

4.1 报错1

/data/software/DNAWorks_ppvm_compile/dnaworks 1_inp.txt > 1_result.txt

Program error:
DNA length is less than 50 nt.

解决办法：

1. dos2unix 1_inp.txt
2. 变量名顺序不对

4.2 报错2

source /etc/profile
python /data/software/DNAWorks_ppvm_compile/dnaworks_v2.py $(sequence).txt $(Oligo length low) $(Oligo length high) '$(Organism)' '$(molecule)'
/data/software/DNAWorks_ppvm_compile/dnaworks inp.txt


python /data/software/DNAWorks_ppvm_compile/dnaworks_v2.py input/test.fa 50 59 H.sapiens PROTEIN
/data/software/DNAWorks_ppvm_compile/dnaworks inp.txt


序列超过256个字符，需要断行。否则内存消耗太大

五、讨论

运算太慢了，没法生成大量的序列