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Here is a short tutorial:

For example, if you want to get sequences upstream of genes coding for adenine transporters:
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: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
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:spirochaetes / gammaproteobacteria/ firmicutes
spiral/rod/coccus etc
non-halophilic/halophilic/moderate halophilic
Q fever

rna_family Family of RNA according to Rfam

Rfam accession: RF00001
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 )




your email