Genomic tools

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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.

Printscreen of the genomics webpage of the Listeriomics website


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. Information about serotype, lineage and the origin of strain isolation were retrieved when possible. For every Listeria gene homologs in other species were searched (INRA ???). Listeria phylogenic tree reconstruction was performed by … (INRA???).

Sequence IDFolder nameNb chromosomeChromosome LengthNB Coding elementChromosome nameDatabaseDatabase folder name (ID)
<a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_003383.1">NC_003383.1</a>Listeria innocua Clip1126228190543Listeria innocua Clip11262 plasmid pLI100, complete sequenceRefSeqListeria_innocua_Clip11262_uid61567
<a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_003212.1">NC_003212.1</a>Listeria innocua Clip11262230112082968Listeria innocua Clip11262, complete genomeRefSeqListeria_innocua_Clip11262_uid61567
<a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_016011.1">NC_016011.1</a>Listeria ivanovii subsp. ivanovii PAM 55129288791911Listeria ivanovii subsp. ivanovii PAM 55, complete genomeRefSeqListeria_ivanovii_PAM_55_uid73473
<a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_017728.1">NC_017728.1</a>Listeria monocytogenes 07PF0776129015622797Listeria monocytogenes 07PF0776 chromosome, complete genomeRefSeqListeria_monocytogenes_07PF0776_uid162185
<a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_013767.1">NC_013767.1</a>Listeria monocytogenes 08-557827705478Listeria monocytogenes 08-5578 plasmid pLM5578, complete sequenceRefSeqListeria_monocytogenes_uid43671
<a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_013766.1">NC_013766.1</a>Listeria monocytogenes 08-5578230322883010Listeria monocytogenes 08-5578 chromosome, complete genomeRefSeqListeria_monocytogenes_uid43671
<a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_013768.1">NC_013768.1</a>Listeria monocytogenes 08-5923129990542966Listeria monocytogenes 08-5923, complete genomeRefSeqListeria_monocytogenes_08_5923_uid43727
<a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_017544.1">NC_017544.1</a>Listeria monocytogenes 10403S129031062814Listeria monocytogenes 10403S chromosome, complete genomeRefSeqListeria_monocytogenes_10403S_uid54461
<a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_018584.1">NC_018584.1</a>Listeria monocytogenes ATCC 19117129518052868Listeria monocytogenes ATCC 19117, complete genomeRefSeqListeria_monocytogenes_ATCC_19117_uid175109
<a href="http://www.ncbi.nlm.nih.gov/nuccore/FM242711.1">FM242711.1</a>Listeria monocytogenes Clip80459 serotype 4b129126901972Listeria monocytogenes Clip80459 serotype 4b complete genomeGenBankListeria_monocytogenes_Clip81459_uid32207
<a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_003210.1">NC_003210.1</a>Listeria monocytogenes EGD-e129445282867Listeria monocytogenes EGD-e chromosome, complete genomeRefSeqListeria_monocytogenes_EGD_e_uid61583
<a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_017547.1">NC_017547.1</a>Listeria monocytogenes Finland 1998128744312762Listeria monocytogenes Finland 1998 chromosome, complete genomeRefSeqListeria_monocytogenes_Finland_1998_uid54443
<a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_017546.1">NC_017546.1</a>Listeria monocytogenes FSL R2-561129738012910Listeria monocytogenes FSL R2-561 chromosome, complete genomeRefSeqListeria_monocytogenes_FSL_R2_561_uid54441
<a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_011660.1">NC_011660.1</a>Listeria monocytogenes HCC23129762122974Listeria monocytogenes HCC23 chromosome, complete genomeRefSeqListeria_monocytogenes_HCC23_uid59203
<a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_017545.1">NC_017545.1</a>Listeria monocytogenes J0161130004642955Listeria monocytogenes J0161 chromosome, complete genomeRefSeqListeria_monocytogenes_J0161_uid54459
<a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_021830.1">NC_021830.1</a>Listeria monocytogenes J1-220130322712985Listeria monocytogenes J1-220, complete genomeRefSeqListeria_monocytogenes_J1_220_uid179735
<a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_021829.1">NC_021829.1</a>Listeria monocytogenes J1816129474602794Listeria monocytogenes J1816, complete genomeRefSeqListeria_monocytogenes_J1816_uid179734
<a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_018642.1">NC_018642.1</a>Listeria monocytogenes L312129123462821Listeria monocytogenes L312, complete genomeRefSeqListeria_monocytogenes_L312_uid175768
<a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_017529.1">NC_017529.1</a>Listeria monocytogenes L99129791982925Listeria monocytogenes L99, complete genomeRefSeqListeria_monocytogenes_serotype_4a_L99_uid161953
<a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_020557.1">NC_020557.1</a>Listeria monocytogenes La111127765173131Listeria monocytogenes La111 complete genomeRefSeqListeria_monocytogenes_La111_uid193768
<a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_017537.1">NC_017537.1</a>Listeria monocytogenes M7129761632977Listeria monocytogenes M7 chromosome, complete genomeRefSeqListeria_monocytogenes_M7_uid162131
<a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_020558.1">NC_020558.1</a>Listeria monocytogenes N53-1127768473150Listeria monocytogenes N53-1 complete genomeRefSeqListeria_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. F2365129051872821Listeria monocytogenes serotype 4b str. F2365 chromosome, complete genomeRefSeqListeria_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. LL195129046622838Listeria monocytogenes serotype 4b str. LL195, complete genomeRefSeqListeria_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. SLCC248225010055Listeria monocytogenes serotype 7 str. SLCC2482 plasmid pLM7UG1, complete sequenceRefSeqListeria_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. SLCC2482229366892874Listeria monocytogenes serotype 7 str. SLCC2482, complete genomeRefSeqListeria_monocytogenes_serotype_7_SLCC2482_uid174871
<a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_018889.1">NC_018889.1</a>Listeria monocytogenes SLCC237225010054Listeria monocytogenes SLCC2372 plasmid pLM1-2cUG1, complete sequenceRefSeqListeria_monocytogenes_SLCC2372_uid174872
<a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_018588.1">NC_018588.1</a>Listeria monocytogenes SLCC2372229728102936Listeria monocytogenes SLCC2372, complete genomeRefSeqListeria_monocytogenes_SLCC2372_uid174872
<a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_018590.1">NC_018590.1</a>Listeria monocytogenes SLCC2376128401852755Listeria monocytogenes SLCC2376, complete genomeRefSeqListeria_monocytogenes_SLCC2376_uid175111
<a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_018585.1">NC_018585.1</a>Listeria monocytogenes SLCC2378129413602874Listeria monocytogenes SLCC2378, complete genomeRefSeqListeria_monocytogenes_SLCC2378_uid175105
<a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_018589.1">NC_018589.1</a>Listeria monocytogenes SLCC2479129721722935Listeria monocytogenes SLCC2479, complete genomeRefSeqListeria_monocytogenes_SLCC2479_uid175108
<a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_018586.1">NC_018586.1</a>Listeria monocytogenes SLCC2540129769582907Listeria monocytogenes SLCC2540, complete genomeRefSeqListeria_monocytogenes_SLCC2540_uid175106
<a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_014495.1">NC_014495.1</a>Listeria monocytogenes SLCC275525778063Listeria monocytogenes SLCC2755 plasmid pLM1-2bUG1, complete sequenceRefSeqListeria_monocytogenes_serotype_1_2b_SLCC2755_uid52455
<a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_018587.1">NC_018587.1</a>Listeria monocytogenes SLCC2755229661462877Listeria monocytogenes SLCC2755, complete genomeRefSeqListeria_monocytogenes_serotype_1_2b_SLCC2755_uid52455
<a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_018592.1">NC_018592.1</a>Listeria monocytogenes SLCC5850129071422865Listeria monocytogenes SLCC5850, complete genomeRefSeqListeria_monocytogenes_SLCC5850_uid175110
<a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_018593.1">NC_018593.1</a>Listeria monocytogenes SLCC7179128822342826Listeria monocytogenes SLCC7179, complete genomeRefSeqListeria_monocytogenes_SLCC7179_uid175107
<a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_021823.1">NC_021823.1</a>Listeria monocytogenes strain C1-387129889472953Listeria monocytogenes strain C1-387, complete genomeRefSeqListeria_monocytogenes_uid212977
<a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_022046.1">NC_022046.1</a>Listeria monocytogenes strain J177625580471Listeria monocytogenes strain J1776 plasmid, complete sequenceRefSeqListeria_monocytogenes_uid212977
<a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_021839.1">NC_021839.1</a>Listeria monocytogenes strain J1776229537192902Listeria monocytogenes strain J1776, complete genomeRefSeqListeria_monocytogenes_uid212977
<a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_022047.1">NC_022047.1</a>Listeria monocytogenes strain J181725580471Listeria monocytogenes strain J1817 plasmid, complete sequenceRefSeqListeria_monocytogenes_uid212977
<a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_021827.1">NC_021827.1</a>Listeria monocytogenes strain J1817229537162903Listeria monocytogenes strain J1817, complete genomeRefSeqListeria_monocytogenes_uid212977
<a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_022051.1">NC_022051.1</a>Listeria monocytogenes strain J192625580371Listeria monocytogenes strain J1926 plasmid, complete sequenceRefSeqListeria_monocytogenes_uid212977
<a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_021840.1">NC_021840.1</a>Listeria monocytogenes strain J1926229537082899Listeria monocytogenes strain J1926, complete genomeRefSeqListeria_monocytogenes_uid212977
<a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_021837.1">NC_021837.1</a>Listeria monocytogenes strain J2-031129589082924Listeria monocytogenes strain J2-031, complete genomeRefSeqListeria_monocytogenes_uid212977
<a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_021824.1">NC_021824.1</a>Listeria monocytogenes strain J2-064129432182865Listeria monocytogenes strain J2-064, complete genomeRefSeqListeria_monocytogenes_uid212977
<a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_021825.1">NC_021825.1</a>Listeria monocytogenes strain J2-1091129818862912Listeria monocytogenes strain J2-1091, complete genomeRefSeqListeria_monocytogenes_uid212977
<a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_022045.1">NC_022045.1</a>Listeria monocytogenes strain N1-011A2148959165Listeria monocytogenes strain N1-011A plasmid, complete sequenceRefSeqListeria_monocytogenes_uid212977
<a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_021826.1">NC_021826.1</a>Listeria monocytogenes strain N1-011A230943423059Listeria monocytogenes strain N1-011A, complete genomeRefSeqListeria_monocytogenes_uid212977
<a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_021828.1">NC_021828.1</a>Listeria monocytogenes strain R2-50225755762Listeria monocytogenes strain R2-502 plasmid, complete sequenceRefSeqListeria_monocytogenes_uid212977
<a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_021838.1">NC_021838.1</a>Listeria monocytogenes strain R2-502230340432984Listeria monocytogenes strain R2-502, complete genomeRefSeqListeria_monocytogenes_uid212977
<a href="http://www.ncbi.nlm.nih.gov/nuccore/FN557490.1">FN557490.1</a>Listeria seeligeri serovar 1-2b str. SLCC3954127976362722Listeria seeligeri serovar 1/2b str. SLCC3954 complete genomeGenBankListeria_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. SLCC5334128141302780Listeria welshimeri serovar 6b str. SLCC5334 complete genomeGenBankListeria_welshimeri_serovar_6b_SLCC5334_uid13443
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