RiboGap

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Here is a short tutorial:

For example, if you want to get intergenic sequences which have a specific noncoding RNA like "TPP" in specfic genome like "NC_000913":
First select the checkboxes for:

"DNA fragment" or/and "description" in the "fragment" section (because this is where you find the information on chromosome)
"start", "end", "strand", "sequence" in the "gap5" section (because this is where you will get the sequence and other related information for the region in 5-prime of the genes)
"description", in the "RNA familly " section (because this is where you will get the sequence RNA known)
"start", "end", "strand", in the "RNA_known" section (because this is where you will get the RNA positions for Known RNA)

After, choose the condition to which you want to limit your search:

Choose "description" of the "RNA_familly " section, choose "find the pattern" and write "TPP".
Choose "DNA fragment" of the "fragment " section, choose "find the pattern" and write "NC_000913".

Please select a field:

Field		Explanation or Example

cdd		Conserved domains

cdd_id cdd_accession cdd_name description		ex: 116891 example: pfam05377 or cd06578 or TIGR01188... name of conserved domains like HemD nickel ABC transporter, nickel/metallophore periplasmic binding protein

cds		Coding sequence

accession gene DNA_seq locus_tag product translation gi start end strand		protein accession like NP_038276.1 gene name like rhlA DNA sequence of gene (No information avaibale for now!!!) ex:Marme_0002 ex:Mg transporter amino acid sequence protein gi like: 326793324 start position end position, strand direction of the gene relative to chromosome

fragment		Chromosome information

DNA fragment frag_gi length is_circular strain chromosome plasmid GC gene_num IGR_length IGR_GC IGR_median organism_id taxonomy description		Refseq accession number like NC_000913 gi of Refseq accession like 158421624 length of chromosome true/false strain information like "Newman" chromosome if exist in database plasmid if exist in database GC % like 52.17 number of genes in chromosome like: 4934 total length of intergenic sequences GC % in intergenic sequences median size of intergenic sequences project id of organism according to NCBI bacteria; elusimicrobia; environmental samples Staphylococcus aureus subsp. aureus str. Newman

gap3		sequence information for 3-prime-UTR

start end strand sequence size		start position of 3 prime-UTR end position of 3 prime-UTR strand direction of the corresponding gene sequence of 3 prime-UTR in the same strand as the gene size of of 3 prime-UTR

gap5		Sequence information for 5-prime-UTR

start end strand sequence size		start position of 5 prime-UTR end position of 5 prime-UTR strand direction of the corresponding gene sequence of 5 prime-UTR in same strand as the gene size of 5 prime-UTR

operon		Operon

operon_id operon_name locus_tag description		CO143545(Conserved) / KO143545(Known) / PR143545 (Predicted) name of operon like virRS ex:Marme_0001, Marme_0002 arylesterase --> hypothetical protein --> peptidase

organism		Organism

organism_id tax_id organism kingdom tax_group gram shape arrangement endospore motility salinity oxygen habitat temp_range optimal_temp pathogenic_in disease		given Id to Organism like "3" taxonomy id according to NCBI like 224326 name of organism like Borrelia burgdorferi B31 ex:bacteria ex:spirochaetes / gammaproteobacteria/ firmicutes +/- spiral/rod/coccus etc single/pairs/chains no/yes no/yes non-halophilic/halophilic/moderate halophilic anaerobic/aerobic/facultative/microaerophilic aquatic/multiple/host-associated mesophilic/psychrophilic/thermophilic/hyperthermophilic 30-42/25-30/25-40/etc human/animal/plant/insect Q fever

rna_family		Family of RNA according to Rfam

fam_id fam_name description type note		Rfam accession: RF00001 5S_rRNA 5S ribosomal RNA gene; rRNA some description

rna_known		Known RNA according to Rfam

start end strand		start position of RNA end position of RNA strand of RNA

Write down your own query: (query of MySQL)

Select a file in infernal foramt (result of cmaling without stockholm sequences )

Infernal in the following format: gi|384505696|ref|NC_017301.1|/884571-884729/B22.19/E0.00014/GC57

Condition:

result_number:

Email:

your email

Welcome to the website of RiboGap

Home | Default_search | Advanced_Search | Contact | Help

Here is a short tutorial:

For example, if you want to get intergenic sequences which have a specific noncoding RNA like "TPP" in specfic genome like "NC_000913": First select the checkboxes for:

"DNA fragment" or/and "description" in the "fragment" section (because this is where you find the information on chromosome)

"start", "end", "strand", "sequence" in the "gap5" section (because this is where you will get the sequence and other related information for the region in 5-prime of the genes)

"description", in the "RNA familly " section (because this is where you will get the sequence RNA known)

"start", "end", "strand", in the "RNA_known" section (because this is where you will get the RNA positions for Known RNA)

After, choose the condition to which you want to limit your search:

Choose "description" of the "RNA_familly " section, choose "find the pattern" and write "TPP".

Choose "DNA fragment" of the "fragment " section, choose "find the pattern" and write "NC_000913".

Please select a field:

For example, if you want to get intergenic sequences which have a specific noncoding RNA like "TPP" in specfic genome like "NC_000913":
First select the checkboxes for: