E. coli genomes: Difference between revisions

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   wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_UTI89/NC_007946.gbk
   wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_UTI89/NC_007946.gbk
  wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_APEC_O1/NC_008253.gbk
   wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_APEC_O1/NC_008563.gbk
   wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_APEC_O1/NC_008563.gbk
  wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_536/NC_008253.gbk
  wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_K_12_substr__W3110/AC_000091.gbk
  wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_CFT073/NC_004431.gbk
  wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_E24377A/NC_009801.gbk
  wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_HS/NC_009800.gbk
  wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_K_12_substr__MG1655/NC_000913.gbk
  wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_O157H7/NC_002695.gbk
  wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_O157H7_EDL933/NC_002655.gbk
  wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Shigella_sonnei_Ss046/NC_007384.gbk
  wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Shigella_flexneri_5_8401/NC_008258.gbk
  wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Shigella_flexneri_2a_2457T/NC_004741.gbk
  wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Shigella_flexneri_2a/NC_004337.gbk
  wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Shigella_dysenteriae/NC_007606.gbk
  wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Shigella_boydii_Sb227/NC_007613.gbk


  wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_0127_H6_E2348_69/NC_011601.gbk


  wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_55989/NC_011748.gbk
  wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_C_ATCC_8739/NC_010468.gbk
  wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_ED1a/NC_011745.gbk
  wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_IAI1/NC_011741.gbk
  wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_IAI39/NC_011750.gbk
  wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_K_12_substr__DH10B/NC_010473.gbk
  wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_O157_H7_EC4115/NC_011353.gbk
  wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_S88/NC_011742.gbk
  wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_SE11/NC_011415.gbk
  wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_SMS_3_5/NC_010498.gbk
  wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_UMN026/NC_011751.gbk
  wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Shigella_boydii_CDC_3083_94/NC_010658.gbk


Currently it appears that only version 1.4.2 of the JRE (Java Runtime Environment) is installed, which is not suitable for all applications. To use the newer version of JRE, you need to specify the full path to the java executable that is installed in the home directory e.g. instead of
  mv NC_007946.gbk Ec_UTI89.gbk
   java app.jar
  mv NC_008563.gbk Ec_APEC_O1.gbk 
use
  mv NC_008253.gbk Ec_536.gbk
   /home/e.skippington/Programs/java/jre1.6.0_07/bin/java app.jar
  mv AC_000091.gbk Ec_W3110.gbk
  mv NC_004431.gbk Ec_CFT073.gbk
  mv NC_009801.gbk Ec_24377A.gbk
  mv NC_009800.gbk Ec_HS.gbk
  mv NC_000913.gbk Ec_K12.gbk
  mv NC_002695.gbk Ec_O157_Sakai.gbk
  mv NC_002655.gbk Ec_O157_EDL933.gbk
  mv NC_007384.gbk Ss_Ss046.gbk
  mv NC_008258.gbk Sf_5_8401.gbk
   mv NC_004741.gbk Sf_2a_2457T.gbk
  mv NC_004337.gbk Sf_2a_301.gbk
   mv NC_007606.gbk Sd_Sd197.gbk
  mv NC_007613.gbk Sb_Sb227.gbk


This has been temporarily fixed by creating a symlink in ~/bin/ of java pointing to the new version of java.
  mv NC_011601.gbk Ec_2348_69.gbk
 
  mv NC_011748.gbk Ec_55989.gbk
  mv NC_010468.gbk Ec_C_ATCC_8739.gbk
  mv NC_011745.gbk Ec_ED1a.gbk
  mv NC_011741.gbk Ec_IAI1.gbk
  mv NC_011750.gbk Ec_IAI39.gbk
  mv NC_010473.gbk Ec_DH10B.gbk
  mv NC_011353.gbk Ec_EC4115.gbk
  mv NC_011742.gbk Ec_S88.gbk
  mv NC_011415.gbk Ec_SE11.gbk
  mv NC_010498.gbk Ec_SMS_3_5.gbk
  mv NC_011751.gbk Ec_UMN026.gbk
  mv NC_010658.gbk Sb_CDC_3083_94.bk
 
 
 
  wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_536/NC_008253.gbk
  wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_55989/NC_011748.gbk
  wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_APEC_O1/NC_008563.gbk
  wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_C_ATCC_8739/NC_010468.gbk
  wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_CFT073/NC_004431.gbk
  wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_0127_H6_E2348_69/NC_011601.gbk
  wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_E24377A/NC_009801.gbk
  wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_ED1a/NC_011745.gbk
  wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_HS/NC_009800.gbk
  wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_IAI1/NC_011741.gbk
  wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_IAI39/NC_011750.gbk
  wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_O157H7_EDL933/NC_002655.gbk
  wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_O157H7/NC_002695.gbk
  wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_S88/NC_011742.gbk
  wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_SE11/NC_011415.gbk
  wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_SMS_3_5/NC_010498.gbk
  wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_UMN026/NC_011751.gbk
  wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_UTI89/NC_007946.gbk
  wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_K_12_substr__MG1655/NC_000913.gbk
  wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_K_12_substr__W3110/AC_000091.gbk
  wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Shigella_boydii_CDC_3083_94/NC_010658.gbk
  wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Shigella_boydii_Sb227/NC_007613.gbk
  wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Shigella_dysenteriae/NC_007606.gbk
  wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Shigella_flexneri_2a_2457T/NC_004741.gbk
  wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Shigella_flexneri_2a/NC_004337.gbk
  wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Shigella_flexneri_5_8401/NC_008258.gbk
  wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Shigella_sonnei_Ss046/NC_007384.gbk

Latest revision as of 23:14, 27 October 2009

E. coli/Shigella genomes

Downloaded 14/5/09 

 wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_UTI89/NC_007946.gbk
 wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_APEC_O1/NC_008563.gbk
 wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_536/NC_008253.gbk
 wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_K_12_substr__W3110/AC_000091.gbk
 wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_CFT073/NC_004431.gbk
 wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_E24377A/NC_009801.gbk
 wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_HS/NC_009800.gbk
 wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_K_12_substr__MG1655/NC_000913.gbk
 wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_O157H7/NC_002695.gbk
 wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_O157H7_EDL933/NC_002655.gbk
 wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Shigella_sonnei_Ss046/NC_007384.gbk
 wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Shigella_flexneri_5_8401/NC_008258.gbk
 wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Shigella_flexneri_2a_2457T/NC_004741.gbk
 wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Shigella_flexneri_2a/NC_004337.gbk
 wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Shigella_dysenteriae/NC_007606.gbk
 wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Shigella_boydii_Sb227/NC_007613.gbk

 wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_0127_H6_E2348_69/NC_011601.gbk

 wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_55989/NC_011748.gbk
 wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_C_ATCC_8739/NC_010468.gbk
 wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_ED1a/NC_011745.gbk
 wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_IAI1/NC_011741.gbk
 wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_IAI39/NC_011750.gbk
 wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_K_12_substr__DH10B/NC_010473.gbk
 wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_O157_H7_EC4115/NC_011353.gbk
 wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_S88/NC_011742.gbk
 wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_SE11/NC_011415.gbk
 wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_SMS_3_5/NC_010498.gbk
 wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_UMN026/NC_011751.gbk
 wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Shigella_boydii_CDC_3083_94/NC_010658.gbk

 mv NC_007946.gbk Ec_UTI89.gbk 
 mv NC_008563.gbk Ec_APEC_O1.gbk  
 mv NC_008253.gbk Ec_536.gbk
 mv AC_000091.gbk Ec_W3110.gbk
 mv NC_004431.gbk Ec_CFT073.gbk
 mv NC_009801.gbk Ec_24377A.gbk
 mv NC_009800.gbk Ec_HS.gbk
 mv NC_000913.gbk Ec_K12.gbk
 mv NC_002695.gbk Ec_O157_Sakai.gbk
 mv NC_002655.gbk Ec_O157_EDL933.gbk
 mv NC_007384.gbk Ss_Ss046.gbk
 mv NC_008258.gbk Sf_5_8401.gbk
 mv NC_004741.gbk Sf_2a_2457T.gbk
 mv NC_004337.gbk Sf_2a_301.gbk
 mv NC_007606.gbk Sd_Sd197.gbk
 mv NC_007613.gbk Sb_Sb227.gbk

 mv NC_011601.gbk Ec_2348_69.gbk

 mv NC_011748.gbk Ec_55989.gbk
 mv NC_010468.gbk Ec_C_ATCC_8739.gbk
 mv NC_011745.gbk Ec_ED1a.gbk
 mv NC_011741.gbk Ec_IAI1.gbk
 mv NC_011750.gbk Ec_IAI39.gbk
 mv NC_010473.gbk Ec_DH10B.gbk
 mv NC_011353.gbk Ec_EC4115.gbk
 mv NC_011742.gbk Ec_S88.gbk
 mv NC_011415.gbk Ec_SE11.gbk
 mv NC_010498.gbk Ec_SMS_3_5.gbk 
 mv NC_011751.gbk Ec_UMN026.gbk
 mv NC_010658.gbk Sb_CDC_3083_94.bk



 wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_536/NC_008253.gbk
 wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_55989/NC_011748.gbk
 wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_APEC_O1/NC_008563.gbk
 wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_C_ATCC_8739/NC_010468.gbk
 wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_CFT073/NC_004431.gbk
 wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_0127_H6_E2348_69/NC_011601.gbk
 wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_E24377A/NC_009801.gbk
 wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_ED1a/NC_011745.gbk
 wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_HS/NC_009800.gbk
 wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_IAI1/NC_011741.gbk
 wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_IAI39/NC_011750.gbk
 wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_O157H7_EDL933/NC_002655.gbk
 wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_O157H7/NC_002695.gbk
 wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_S88/NC_011742.gbk
 wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_SE11/NC_011415.gbk
 wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_SMS_3_5/NC_010498.gbk
 wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_UMN026/NC_011751.gbk
 wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_UTI89/NC_007946.gbk
 wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_K_12_substr__MG1655/NC_000913.gbk
 wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_K_12_substr__W3110/AC_000091.gbk
 wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Shigella_boydii_CDC_3083_94/NC_010658.gbk
 wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Shigella_boydii_Sb227/NC_007613.gbk
 wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Shigella_dysenteriae/NC_007606.gbk
 wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Shigella_flexneri_2a_2457T/NC_004741.gbk
 wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Shigella_flexneri_2a/NC_004337.gbk
 wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Shigella_flexneri_5_8401/NC_008258.gbk
 wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Shigella_sonnei_Ss046/NC_007384.gbk
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