【5.4.1】密码子优化本地化不靠谱的软件

一、dtailor

https://sourceforge.net/projects/dtailor/

wget -c https://sourceforge.net/projects/dtailor/files/latest/download

unzip  dtailor.src.zip
cd /mnt/nfs/data/user/sam/project/codon_optimization/lib/D-Tailor

报错：

UNAFold — http://mfold.rna.albany.edu/?q=DINAMelt/software 学术也得 $200.00哦

放弃了，改起来太费劲了

二、eugene

wget -c  http://bioinformatics.ua.pt/eugene/Eugene.zip
unzip Eugene.zip
cd Eugene/

没跑起来。。。

三、codon_optimization 2016

https://github.com/Kange2014/codon_optimization

四、codon_optimization 2018

https://github.com/yutaka-saito/codon_optimization

4.1 安装

#RNAstructure:
http://rna.urmc.rochester.edu/RNAstructureDownload.html

wget -c http://rna.urmc.rochester.edu/Releases/current/RNAstructureSource.tgz

tar xvfm RNAstructureSource.tgz
make install all 

vim /etc/profile 

export PATH=/data/software/rna/RNAstructure/exe:$PATH
export DATAPATH=/data/software/rna/RNAstructure/data_tables

#
cd /mnt/nfs/data/user/sam/project/codon_optimization/lib/
git clone https://github.com/yutaka-saito/codon_optimization.git

4.2 使用

cd /mnt/nfs/data/user/sam/project/codon_optimization/lib/codon_optimization


mkdir test
codon_optimization_HC.pl misc/translation_table_11 misc/codon_frequency_Rery seq/gi_21219378.fa utr/pTip.fa test > result.txt


[sam@g02 codon_optimization]$ cat misc/translation_table_11
    AAs  = FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
  Starts = ---M------**--*----M------------MMMM---------------M------------
  Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
  Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
  Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG


[sam@g02 codon_optimization]$ cat misc/codon_frequency_Rery
UUU  4.0(   939)  UCU  4.4(  1019)  UAU  4.2(   985)  UGU  2.3(   532)
UUC 25.6(  5947)  UCC 15.2(  3536)  UAC 16.5(  3845)  UGC  7.1(  1649)
UUA  1.1(   251)  UCA  5.3(  1241)  UAA  0.4(    98)  UGA  2.4(   568)
UUG 14.1(  3288)  UCG 18.9(  4406)  UAG  0.6(   151)  UGG 17.0(  3957)

CUU  7.9(  1849)  CCU  6.9(  1612)  CAU  6.7(  1556)  CGU 10.8(  2517)
CUC 33.9(  7883)  CCC 16.1(  3755)  CAC 17.5(  4078)  CGC 27.2(  6330)
CUA  3.4(   784)  CCA  6.7(  1551)  CAA  9.6(  2225)  CGA 12.5(  2899)
CUG 32.7(  7598)  CCG 26.8(  6226)  CAG 21.3(  4964)  CGG 17.1(  3984)

AUU  6.8(  1575)  ACU  7.2(  1673)  AAU  5.5(  1282)  AGU  5.5(  1268)
AUC 37.1(  8629)  ACC 32.1(  7469)  AAC 17.8(  4140)  AGC 13.5(  3131)
AUA  2.1(   497)  ACA  8.5(  1966)  AAA  8.1(  1878)  AGA  2.7(   636)
AUG 19.5(  4537)  ACG 16.2(  3778)  AAG 17.7(  4111)  AGG  4.1(   943)

GUU  9.9(  2301)  GCU 14.3(  3320)  GAU 18.3(  4264)  GGU 17.1(  3971)
GUC 38.7(  8995)  GCC 44.0( 10241)  GAC 42.0(  9777)  GGC 33.4(  7765)
GUA  5.9(  1384)  GCA 22.5(  5235)  GAA 25.4(  5907)  GGA 17.2(  4005)
GUG 26.4(  6136)  GCG 39.1(  9084)  GAG 30.9(  7179)  GGG 14.3(  3321)


#测试
time ./codon_optimization_HC.pl misc/translation_table_11 misc/codon_frequency_Rery test/test.fa utr/pTip.fa test > test/result.txt

五、Codon Optimizer 2012 （因为也是CAI)

http://www.cs.ubc.ca/labs/beta/Projects/codon-optimizer/

A software tool to remove forbidden motifs, add desirable motifs, and optimize codon usage of a protein sequence according to the CAI measure.

安装

cd /data/user/sam/project/codon_optimization/lib
wget -c http://www.cs.ubc.ca/labs/beta/Projects/codon-optimizer/downloads/codon-optimizer-0.1.zip

unzip codon-optimizer-0.1.zip
cd codon-optimizer-0.1
./configure --prefix=/data/user/sam/project/codon_optimization/lib/codon-optimizer
make
make install

使用 ./codon-optimizer

Usage: codon-optimizer [options] <fasta_file>

Allowed options:

Generic:
  -h [ --help ]         produce this help message

Design Specifications:
  -s [ --start-index ] arg (=1)                              first index in FASTA file of sequences to optimize
  -e [ --end-index ] arg (=1)                                last index in FASTA file of sequences to optimize
  -f [ --forbidden-motif-file ] arg                          a newline separated file containing forbidden motifs
  -d [ --desired-motif-file ] arg                            a newline separated file containing desired motifs
                                                             
Other:                                                       
  -o [ --optimized-sequence-file ] arg (=optimized.fasta)    output file for optimized sequences
  -t [ --trace-file ] arg (=optimized.trace)                 trace file for optimized sequences
  
  

cd /data/user/sam/project/codon_optimization/lib/codon-optimizer-0.1/test
../codon-optimizer -f ../data/motifs/forbidden.cpg -d ../data/motifs/desirable.cpg test.fa -o optimized.fasta -t optimized.trace -s 1 -e 3



optimized.trace :

#Warning: sequence 1 length is not a multiple of 3.  It has been truncated.
#seq_id  length  CAI_before  Forbidden_before  Desirable_before  CAI_after  Forbidden_after  Desirable_after  CPU_runtime
1        351     0.588861    18                2                 0.868277   0                21               0.050000

问题：

1. 如何去选择参考基因组
2. 只生成一个结果？