Optimus

Optimus is the supplementary website/database to the paper (toLink). Users can retrieve conserved gene cluster data from a number of microbial genomes as well as perform searches based on genomic context. See paper for detailed description of the method.

Reference: Yu Zheng1, Brian Anton1, Richard Roberts2, Simon Kasif1 (2005) xxx 1. Bioinformatics Graduate Program, Boston University 2. New England Biolabs Inc.

Note: you may need to turn off pop-up blocking programs.

1.View conserved clusters in microbial genomes
Select organism
Aeropyrum_pernixAgrobacterium_tumefaciens_C58Agrobacterium_tumefaciens_C58_UWashAquifex_aeolicusArchaeoglobus_fulgidusBacillus_haloduransBacillus_subtilisBorrelia_burgdorferiBrucella_melitensisBuchnera_spCampylobacter_jejuniCaulobacter_crescentusChlamydia_muridarumChlamydia_trachomatisChlamydophila_pneumoniae_AR39Chlamydophila_pneumoniae_CWL029Chlamydophila_pneumoniae_J138Clostridium_acetobutylicumClostridium_perfringensDeinococcus_radioduransEscherichia_coli_K12Escherichia_coli_O157H7_EDL933Escherichia_coli_O157H7Fusobacterium_nucleatumHaemophilus_influenzaeHalobacterium_spHelicobacter_pylori_26695Helicobacter_pylori_J99Lactococcus_lactisListeria_innocuaListeria_monocytogenesMesorhizobium_lotiMethanobacterium_thermoautotrophicumMethanococcus_jannaschiiMethanopyrus_kandleriMethanosarcina_acetivoransMethanosarcina_mazeiMycobacterium_lepraeMycobacterium_tuberculosis_CDC1551Mycobacterium_tuberculosis_H37RvMycoplasma_genitaliumMycoplasma_pneumoniaeMycoplasma_pulmonisNeisseria_meningitidis_MC58Neisseria_meningitidis_Z2491Nostoc_spPasteurella_multocidaPseudomonas_aeruginosaPyrobaculum_aerophilumPyrococcus_abyssiPyrococcus_horikoshiiRalstonia_solanacearumRickettsia_conoriiRickettsia_prowazekiiSalmonella_typhiSalmonella_typhimurium_LT2Sinorhizobium_melilotiStaphylococcus_aureus_Mu50Staphylococcus_aureus_N315Streptococcus_pneumoniae_R6Streptococcus_pneumoniae_TIGR4Streptococcus_pyogenesStreptococcus_pyogenes_MGAS8232Streptomyces_coelicolorSulfolobus_solfataricusSulfolobus_tokodaiiSynechocystis_PCC6803Thermoanaerobacter_tengcongensisThermoplasma_acidophilumThermoplasma_volcaniumThermotoga_maritimaTreponema_pallidumUreaplasma_urealyticumVibrio_choleraeXanthomonas_campestrisXylella_fastidiosaYersinia_pestisXanthomonas_citriStaphylococcus_aureus_MW2Buchnera_aphidicola_SgChlorobium_tepidum_TLSStreptococcus_pyogenes_MGAS315
Conservation Score Cutoff
2. Search/BLAST Optimus (In construction)
Enter ID(e.g.,1786259)
or,enter keyword(e.g.,'pyruvate dehydrogenase')
(Optimus returns genomic contexts that are related with the input terms)
in  all genomesAeropyrum_pernixAgrobacterium_tumefaciens_C58Agrobacterium_tumefaciens_C58_UWashAquifex_aeolicusArchaeoglobus_fulgidusBacillus_haloduransBacillus_subtilisBorrelia_burgdorferiBrucella_melitensisBuchnera_spCampylobacter_jejuniCaulobacter_crescentusChlamydia_muridarumChlamydia_trachomatisChlamydophila_pneumoniae_AR39Chlamydophila_pneumoniae_CWL029Chlamydophila_pneumoniae_J138Clostridium_acetobutylicumClostridium_perfringensDeinococcus_radioduransEscherichia_coli_K12Escherichia_coli_O157H7_EDL933Escherichia_coli_O157H7Fusobacterium_nucleatumHaemophilus_influenzaeHalobacterium_spHelicobacter_pylori_26695Helicobacter_pylori_J99Lactococcus_lactisListeria_innocuaListeria_monocytogenesMesorhizobium_lotiMethanobacterium_thermoautotrophicumMethanococcus_jannaschiiMethanopyrus_kandleriMethanosarcina_acetivoransMethanosarcina_mazeiMycobacterium_lepraeMycobacterium_tuberculosis_CDC1551Mycobacterium_tuberculosis_H37RvMycoplasma_genitaliumMycoplasma_pneumoniaeMycoplasma_pulmonisNeisseria_meningitidis_MC58Neisseria_meningitidis_Z2491Nostoc_spPasteurella_multocidaPseudomonas_aeruginosaPyrobaculum_aerophilumPyrococcus_abyssiPyrococcus_horikoshiiRalstonia_solanacearumRickettsia_conoriiRickettsia_prowazekiiSalmonella_typhiSalmonella_typhimurium_LT2Sinorhizobium_melilotiStaphylococcus_aureus_Mu50Staphylococcus_aureus_N315Streptococcus_pneumoniae_R6Streptococcus_pneumoniae_TIGR4Streptococcus_pyogenesStreptococcus_pyogenes_MGAS8232Streptomyces_coelicolorSulfolobus_solfataricusSulfolobus_tokodaiiSynechocystis_PCC6803Thermoanaerobacter_tengcongensisThermoplasma_acidophilumThermoplasma_volcaniumThermotoga_maritimaTreponema_pallidumUreaplasma_urealyticumVibrio_choleraeXanthomonas_campestrisXylella_fastidiosaYersinia_pestisXanthomonas_citriStaphylococcus_aureus_MW2Buchnera_aphidicola_SgChlorobium_tepidum_TLSStreptococcus_pyogenes_MGAS315
or, input sequence(FASTA or raw sequence)
(Optimus returns similar/homologous genes with their genomic context)