Welcome to the website of RiboGap
Sorry for this summer's hiatus, our server and backup crashed at the same time! Hopefully, the server will be stable from now on.

Home | Default_search | Advanced_Search | Contact | Help

Here is a short tutorial:

For example, if you want to know RNA known in 5-UTR and associated genes in all the Bacillus
First select the checkboxes for:

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


Please select a field:

Field Explanation or Example


cdd Conserved domains






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












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

















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 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 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






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


organism Organism



















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







Rfam accession: RF00001
5S_rRNA
5S ribosomal RNA
gene; rRNA
some description


rna_known Known RNA according to Rfam





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 )


Condition:










result_number:


Email:

your email