Neisseria Base

Neisseria Base provides access to genomic and proteomic data of various hypervirulent strains of N. meningitidis, the leading cause of bacterial meningitis. Our genomes(M13220_PH_A,M10699_OR_B,M15141_NYC_C,M9261_BF_W135) have been sequenced using 454 pyrosequencing at CDC.

Search Genes By

Quick search help preferences Keywords may include anything related to Neisseria meningitidis. some of the categories for Keywords : Gene name,Feature type,protein Name,Uniprot ID,GO ID, Go term, Domain name. Multiple keywords can be given using comma(,) as delimiter. Example:kinase,protease - To get results for both kinase and protease. By default all the genomes are searched for the given input. user can specify which genomes to search in preferences section. Quick search returns more number of results than any normal search.If you want specific results, please search on spefcific properties as given below.
Keyword
Genomes to search	M13220_PH_A M10699_OR_B M15141_NYC_C M9261_BF_W135 NM_053442 NM_FAM18 NM_MC58 NM_Z2491 NM_alpha14 NM_alpha153 NM_alpha275 PLM15141 Select all Clear all
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Gene information help preferences Gene information includes Gene name:Examples for Gene name are kinase,4Fe-4S bacterial type, adenyalte etc. Gene Length This returns all the genes having length atleast MIN length and atmost MAX length Feature Type Feature of the given gene.The categories are AH_ISLAND,CDS,COG,HGT,IS,tRNA,Virulence. AND is applied if more than one field is given as input. Example:Gene length= min 250 max 500, Feature= COGS shows all the genes that have length between 250 and 500 nucleotides from feature type COG By default all the genomes are searched for the given input. user can specify which genomes to search in preferences section. Multiple gene names can be entered by separating them with a comma(,).
Gene Name
Gene Length (nucleotides)	Min: Max:
Feature Type
Genomes to search	M13220_PH_A M10699_OR_B M15141_NYC_C M9261_BF_W135 NM_053442 NM_FAM18 NM_MC58 NM_Z2491 NM_alpha14 NM_alpha153 NM_alpha275 PLM15141 Select all Clear all
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Protein information help preferences Protein information includes Name of the protein . Example:Transporter, NADH dehydrogenase Molecular weight user can input minimum and maximum molecular weight in kilodaltons to get the results for all the genes that gives proteins with molecular weight between these limits. Iso electric point:The isoelectric point (pI) is the pH at which a particular molecule or surface carries no net electrical charge. Example : 6 Uniprot ID Genes encoding proteins having given uniprot ID Example:Q7DDR9 AND is applied if more than one field is given as input. By default all the genomes are searched for the given input. user can specify which genomes to search in preferences section. Multiple protein names and Unirpot Id's can be entered by separating them with a comma(,).
Protein Name
Molecular weight (kilo Daltons)	Min: Max:
Isoelectric point	Min: Max:
Uniprot ID
Genomes to search	M13220_PH_A M10699_OR_B M15141_NYC_C M9261_BF_W135 NM_053442 NM_FAM18 NM_MC58 NM_Z2491 NM_alpha14 NM_alpha153 NM_alpha275 PLM15141 Select all Clear all
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Transmembrane helices help preferences Search genes based on the encoded proteins having transmembrane helices. AND is applied if more than one field is given as input. By default all the genomes are searched for the given input. user can specify which genomes to search in preferences section.
Number of Transmembrane helices	Min: Max:
Length of transmembrane helix	Min: Max:
Genomes to search	M13220_PH_A M10699_OR_B M15141_NYC_C M9261_BF_W135 NM_053442 NM_FAM18 NM_MC58 NM_Z2491 NM_alpha14 NM_alpha153 NM_alpha275 PLM15141 Select all Clear all
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Gene Ontology help preferences Gene Ontology: The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism. Information on the gene ontology can be found in here GO ID Example-GO:0009103 Example of Go terms -lipopolysaccharide biosynthetic process Go category may be any one of the following :Molecular function,Biological process, cellular component AND is applied if more than one field is given as input. By default all the genomes are searched for the given input. user can specify which genomes to search in preferences section.
GO ID
GO term
GO category
Genomes to search	M13220_PH_A M10699_OR_B M15141_NYC_C M9261_BF_W135 NM_053442 NM_FAM18 NM_MC58 NM_Z2491 NM_alpha14 NM_alpha153 NM_alpha275 PLM15141 Select all Clear all
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SignalP help preferences A signal peptide is a short (3-60 amino acids long) peptide chain that directs the post-translational transport of a protein. Signal peptides may also be called targeting signals, signal sequences, transit peptides, or localization signals. The amino acid sequences of signal peptides direct proteins (which are synthesized in the cytosol) to certain organelles such as the nucleus, mitochondrial matrix, endoplasmic reticulum, chloroplast, apoplast and peroxisome. Some signal peptides are cleaved from the protein by signal peptidase after the proteins are transported. Signalp: SignalP 3.0 server predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive prokaryotes, Gram-negative prokaryotes, and eukaryotes. The method incorporates a prediction of cleavage sites and a signal peptide/non-signal peptide prediction based on a combination of several artificial neural networks and hidden Markov models. For more information on signalp server visit the website : http://www.cbs.dtu.dk/services/SignalP/ AND is applied if more than one field is given as input. By default all the genomes are searched for the given input. user can specify which genomes to search in preferences section.
Having a signal peptide	Yes No
C-score	Max:
mean S-score	Max:
Genomes to search	M13220_PH_A M10699_OR_B M15141_NYC_C M9261_BF_W135 NM_053442 NM_FAM18 NM_MC58 NM_Z2491 NM_alpha14 NM_alpha153 NM_alpha275 PLM15141 Select all Clear all
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InterPro Domain help preferences Find genes whose predicted protein contains a domain from the InterPro set of domain databases. The domain matches are identified by the InterProScan program For more information on Interpro visit the website : http://www.ebi.ac.uk/interpro/tutorial.html AND is applied if more than one field is given as input. By default all the genomes are searched for the given input. user can specify which genomes to search in preferences section. users can specify more than one domain name separated by comma(,).
Domain database
Domain Name
Genomes to search	M13220_PH_A M10699_OR_B M15141_NYC_C M9261_BF_W135 NM_053442 NM_FAM18 NM_MC58 NM_Z2491 NM_alpha14 NM_alpha153 NM_alpha275 PLM15141 Select all Clear all
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Neisseria Base

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