Genomic tools
From Listeriomics Wiki
Genomics webpage
Thanks to Genomics button on the top banner, one can access the genomic webpage which is designed to browse through every complete genome available. One can access strain name, serotype, lineage, and isolation information, along with a complete phylogram of the Listeria strains. By double clicking on a strain the list of annotated genes will appear in a new summary panel.
| Phylogram of all 50 Listeria strains
It gives access the genomic tool which is designed to browse through every complete genome available. One can access strain name, serotype, lineage, and isolation information, along with a complete phylogram of the Listeria strains. By double clicking on a strain the list of annotated genes will appear in a new summary panel. |
| List of all Listeria genomes with strain information available
A summary table shows every dataset available and a precise description of the biological conditions used to generate them. Filters are available to select a particular type of biological condition and data. A vast variety of datasets are available. In total, 4 different types of technology (Gene Expression array, Tiling array, RNASeq, TSS) are included for 7 different Listeria monocytogenes strains grown in 4 different broth media and 7 intracellular conditions. |
Genomics database
The 50 complete Listeria genomes available on NCBI RefSeq and GenBank databases were downloaded and integrated into our database.
| Sequence ID | Folder name | Nb chromosome | Chromosome Length | NB Coding element | Chromosome name | Database | Database folder name (ID) |
|---|---|---|---|---|---|---|---|
| NC_003383.1 | Listeria innocua Clip11262 | 2 | 81905 | 43 | Listeria innocua Clip11262 plasmid pLI100, complete sequence | RefSeq | Listeria_innocua_Clip11262_uid61567 |
| <a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_003212.1">NC_003212.1</a> | Listeria innocua Clip11262 | 2 | 3011208 | 2968 | Listeria innocua Clip11262, complete genome | RefSeq | Listeria_innocua_Clip11262_uid61567 |
| <a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_016011.1">NC_016011.1</a> | Listeria ivanovii subsp. ivanovii PAM 55 | 1 | 2928879 | 1911 | Listeria ivanovii subsp. ivanovii PAM 55, complete genome | RefSeq | Listeria_ivanovii_PAM_55_uid73473 |
| <a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_017728.1">NC_017728.1</a> | Listeria monocytogenes 07PF0776 | 1 | 2901562 | 2797 | Listeria monocytogenes 07PF0776 chromosome, complete genome | RefSeq | Listeria_monocytogenes_07PF0776_uid162185 |
| <a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_013767.1">NC_013767.1</a> | Listeria monocytogenes 08-5578 | 2 | 77054 | 78 | Listeria monocytogenes 08-5578 plasmid pLM5578, complete sequence | RefSeq | Listeria_monocytogenes_uid43671 |
| <a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_013766.1">NC_013766.1</a> | Listeria monocytogenes 08-5578 | 2 | 3032288 | 3010 | Listeria monocytogenes 08-5578 chromosome, complete genome | RefSeq | Listeria_monocytogenes_uid43671 |
| <a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_013768.1">NC_013768.1</a> | Listeria monocytogenes 08-5923 | 1 | 2999054 | 2966 | Listeria monocytogenes 08-5923, complete genome | RefSeq | Listeria_monocytogenes_08_5923_uid43727 |
| <a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_017544.1">NC_017544.1</a> | Listeria monocytogenes 10403S | 1 | 2903106 | 2814 | Listeria monocytogenes 10403S chromosome, complete genome | RefSeq | Listeria_monocytogenes_10403S_uid54461 |
| <a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_018584.1">NC_018584.1</a> | Listeria monocytogenes ATCC 19117 | 1 | 2951805 | 2868 | Listeria monocytogenes ATCC 19117, complete genome | RefSeq | Listeria_monocytogenes_ATCC_19117_uid175109 |
| <a href="http://www.ncbi.nlm.nih.gov/nuccore/FM242711.1">FM242711.1</a> | Listeria monocytogenes Clip80459 serotype 4b | 1 | 2912690 | 1972 | Listeria monocytogenes Clip80459 serotype 4b complete genome | GenBank | Listeria_monocytogenes_Clip81459_uid32207 |
| <a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_003210.1">NC_003210.1</a> | Listeria monocytogenes EGD-e | 1 | 2944528 | 2867 | Listeria monocytogenes EGD-e chromosome, complete genome | RefSeq | Listeria_monocytogenes_EGD_e_uid61583 |
| <a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_017547.1">NC_017547.1</a> | Listeria monocytogenes Finland 1998 | 1 | 2874431 | 2762 | Listeria monocytogenes Finland 1998 chromosome, complete genome | RefSeq | Listeria_monocytogenes_Finland_1998_uid54443 |
| <a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_017546.1">NC_017546.1</a> | Listeria monocytogenes FSL R2-561 | 1 | 2973801 | 2910 | Listeria monocytogenes FSL R2-561 chromosome, complete genome | RefSeq | Listeria_monocytogenes_FSL_R2_561_uid54441 |
| <a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_011660.1">NC_011660.1</a> | Listeria monocytogenes HCC23 | 1 | 2976212 | 2974 | Listeria monocytogenes HCC23 chromosome, complete genome | RefSeq | Listeria_monocytogenes_HCC23_uid59203 |
| <a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_017545.1">NC_017545.1</a> | Listeria monocytogenes J0161 | 1 | 3000464 | 2955 | Listeria monocytogenes J0161 chromosome, complete genome | RefSeq | Listeria_monocytogenes_J0161_uid54459 |
| <a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_021830.1">NC_021830.1</a> | Listeria monocytogenes J1-220 | 1 | 3032271 | 2985 | Listeria monocytogenes J1-220, complete genome | RefSeq | Listeria_monocytogenes_J1_220_uid179735 |
| <a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_021829.1">NC_021829.1</a> | Listeria monocytogenes J1816 | 1 | 2947460 | 2794 | Listeria monocytogenes J1816, complete genome | RefSeq | Listeria_monocytogenes_J1816_uid179734 |
| <a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_018642.1">NC_018642.1</a> | Listeria monocytogenes L312 | 1 | 2912346 | 2821 | Listeria monocytogenes L312, complete genome | RefSeq | Listeria_monocytogenes_L312_uid175768 |
| <a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_017529.1">NC_017529.1</a> | Listeria monocytogenes L99 | 1 | 2979198 | 2925 | Listeria monocytogenes L99, complete genome | RefSeq | Listeria_monocytogenes_serotype_4a_L99_uid161953 |
| <a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_020557.1">NC_020557.1</a> | Listeria monocytogenes La111 | 1 | 2776517 | 3131 | Listeria monocytogenes La111 complete genome | RefSeq | Listeria_monocytogenes_La111_uid193768 |
| <a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_017537.1">NC_017537.1</a> | Listeria monocytogenes M7 | 1 | 2976163 | 2977 | Listeria monocytogenes M7 chromosome, complete genome | RefSeq | Listeria_monocytogenes_M7_uid162131 |
| <a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_020558.1">NC_020558.1</a> | Listeria monocytogenes N53-1 | 1 | 2776847 | 3150 | Listeria monocytogenes N53-1 complete genome | RefSeq | Listeria_monocytogenes_N53_1_uid193767 |
| <a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_002973.6">NC_002973.6</a> | Listeria monocytogenes serotype 4b str. F2365 | 1 | 2905187 | 2821 | Listeria monocytogenes serotype 4b str. F2365 chromosome, complete genome | RefSeq | Listeria_monocytogenes_serotype_4b_F2365_uid57689 |
| <a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_019556.1">NC_019556.1</a> | Listeria monocytogenes serotype 4b str. LL195 | 1 | 2904662 | 2838 | Listeria monocytogenes serotype 4b str. LL195, complete genome | RefSeq | Listeria_monocytogenes_serotype_4b_LL195_uid182103 |
| <a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_018888.1">NC_018888.1</a> | Listeria monocytogenes serotype 7 str. SLCC2482 | 2 | 50100 | 55 | Listeria monocytogenes serotype 7 str. SLCC2482 plasmid pLM7UG1, complete sequence | RefSeq | Listeria_monocytogenes_serotype_7_SLCC2482_uid174871 |
| <a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_018591.1">NC_018591.1</a> | Listeria monocytogenes serotype 7 str. SLCC2482 | 2 | 2936689 | 2874 | Listeria monocytogenes serotype 7 str. SLCC2482, complete genome | RefSeq | Listeria_monocytogenes_serotype_7_SLCC2482_uid174871 |
| <a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_018889.1">NC_018889.1</a> | Listeria monocytogenes SLCC2372 | 2 | 50100 | 54 | Listeria monocytogenes SLCC2372 plasmid pLM1-2cUG1, complete sequence | RefSeq | Listeria_monocytogenes_SLCC2372_uid174872 |
| <a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_018588.1">NC_018588.1</a> | Listeria monocytogenes SLCC2372 | 2 | 2972810 | 2936 | Listeria monocytogenes SLCC2372, complete genome | RefSeq | Listeria_monocytogenes_SLCC2372_uid174872 |
| <a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_018590.1">NC_018590.1</a> | Listeria monocytogenes SLCC2376 | 1 | 2840185 | 2755 | Listeria monocytogenes SLCC2376, complete genome | RefSeq | Listeria_monocytogenes_SLCC2376_uid175111 |
| <a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_018585.1">NC_018585.1</a> | Listeria monocytogenes SLCC2378 | 1 | 2941360 | 2874 | Listeria monocytogenes SLCC2378, complete genome | RefSeq | Listeria_monocytogenes_SLCC2378_uid175105 |
| <a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_018589.1">NC_018589.1</a> | Listeria monocytogenes SLCC2479 | 1 | 2972172 | 2935 | Listeria monocytogenes SLCC2479, complete genome | RefSeq | Listeria_monocytogenes_SLCC2479_uid175108 |
| <a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_018586.1">NC_018586.1</a> | Listeria monocytogenes SLCC2540 | 1 | 2976958 | 2907 | Listeria monocytogenes SLCC2540, complete genome | RefSeq | Listeria_monocytogenes_SLCC2540_uid175106 |
| <a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_014495.1">NC_014495.1</a> | Listeria monocytogenes SLCC2755 | 2 | 57780 | 63 | Listeria monocytogenes SLCC2755 plasmid pLM1-2bUG1, complete sequence | RefSeq | Listeria_monocytogenes_serotype_1_2b_SLCC2755_uid52455 |
| <a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_018587.1">NC_018587.1</a> | Listeria monocytogenes SLCC2755 | 2 | 2966146 | 2877 | Listeria monocytogenes SLCC2755, complete genome | RefSeq | Listeria_monocytogenes_serotype_1_2b_SLCC2755_uid52455 |
| <a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_018592.1">NC_018592.1</a> | Listeria monocytogenes SLCC5850 | 1 | 2907142 | 2865 | Listeria monocytogenes SLCC5850, complete genome | RefSeq | Listeria_monocytogenes_SLCC5850_uid175110 |
| <a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_018593.1">NC_018593.1</a> | Listeria monocytogenes SLCC7179 | 1 | 2882234 | 2826 | Listeria monocytogenes SLCC7179, complete genome | RefSeq | Listeria_monocytogenes_SLCC7179_uid175107 |
| <a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_021823.1">NC_021823.1</a> | Listeria monocytogenes strain C1-387 | 1 | 2988947 | 2953 | Listeria monocytogenes strain C1-387, complete genome | RefSeq | Listeria_monocytogenes_uid212977 |
| <a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_022046.1">NC_022046.1</a> | Listeria monocytogenes strain J1776 | 2 | 55804 | 71 | Listeria monocytogenes strain J1776 plasmid, complete sequence | RefSeq | Listeria_monocytogenes_uid212977 |
| <a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_021839.1">NC_021839.1</a> | Listeria monocytogenes strain J1776 | 2 | 2953719 | 2902 | Listeria monocytogenes strain J1776, complete genome | RefSeq | Listeria_monocytogenes_uid212977 |
| <a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_022047.1">NC_022047.1</a> | Listeria monocytogenes strain J1817 | 2 | 55804 | 71 | Listeria monocytogenes strain J1817 plasmid, complete sequence | RefSeq | Listeria_monocytogenes_uid212977 |
| <a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_021827.1">NC_021827.1</a> | Listeria monocytogenes strain J1817 | 2 | 2953716 | 2903 | Listeria monocytogenes strain J1817, complete genome | RefSeq | Listeria_monocytogenes_uid212977 |
| <a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_022051.1">NC_022051.1</a> | Listeria monocytogenes strain J1926 | 2 | 55803 | 71 | Listeria monocytogenes strain J1926 plasmid, complete sequence | RefSeq | Listeria_monocytogenes_uid212977 |
| <a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_021840.1">NC_021840.1</a> | Listeria monocytogenes strain J1926 | 2 | 2953708 | 2899 | Listeria monocytogenes strain J1926, complete genome | RefSeq | Listeria_monocytogenes_uid212977 |
| <a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_021837.1">NC_021837.1</a> | Listeria monocytogenes strain J2-031 | 1 | 2958908 | 2924 | Listeria monocytogenes strain J2-031, complete genome | RefSeq | Listeria_monocytogenes_uid212977 |
| <a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_021824.1">NC_021824.1</a> | Listeria monocytogenes strain J2-064 | 1 | 2943218 | 2865 | Listeria monocytogenes strain J2-064, complete genome | RefSeq | Listeria_monocytogenes_uid212977 |
| <a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_021825.1">NC_021825.1</a> | Listeria monocytogenes strain J2-1091 | 1 | 2981886 | 2912 | Listeria monocytogenes strain J2-1091, complete genome | RefSeq | Listeria_monocytogenes_uid212977 |
| <a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_022045.1">NC_022045.1</a> | Listeria monocytogenes strain N1-011A | 2 | 148959 | 165 | Listeria monocytogenes strain N1-011A plasmid, complete sequence | RefSeq | Listeria_monocytogenes_uid212977 |
| <a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_021826.1">NC_021826.1</a> | Listeria monocytogenes strain N1-011A | 2 | 3094342 | 3059 | Listeria monocytogenes strain N1-011A, complete genome | RefSeq | Listeria_monocytogenes_uid212977 |
| <a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_021828.1">NC_021828.1</a> | Listeria monocytogenes strain R2-502 | 2 | 57557 | 62 | Listeria monocytogenes strain R2-502 plasmid, complete sequence | RefSeq | Listeria_monocytogenes_uid212977 |
| <a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_021838.1">NC_021838.1</a> | Listeria monocytogenes strain R2-502 | 2 | 3034043 | 2984 | Listeria monocytogenes strain R2-502, complete genome | RefSeq | Listeria_monocytogenes_uid212977 |
| <a href="http://www.ncbi.nlm.nih.gov/nuccore/FN557490.1">FN557490.1</a> | Listeria seeligeri serovar 1-2b str. SLCC3954 | 1 | 2797636 | 2722 | Listeria seeligeri serovar 1/2b str. SLCC3954 complete genome | GenBank | Listeria_seeligeri_serovar_1_2b_SLCC3954_uid41123 |
| <a href="http://www.ncbi.nlm.nih.gov/nuccore/AM263198.1">AM263198.1</a> | Listeria welshimeri serovar 6b str. SLCC5334 | 1 | 2814130 | 2780 | Listeria welshimeri serovar 6b str. SLCC5334 complete genome | GenBank | Listeria_welshimeri_serovar_6b_SLCC5334_uid13443 |
