DBSCR - about this database

Database of transcriptional regulation in Streptomyces coelicolor and its closest relatives

Home

DBSCR

DBSCR is a referenced database of published transcriptional regulation events mainly in Streptomyces coelicolor A3(2) and its closest relatives, such as S. griseus, S. peucetius, S. albogriseolus, S. vinezuelae, and S. cacaoi. It is essentially a compilation of transcription factors with their regulated genes as well as their recognition sequences, which were experimentally characterized and reported in the literature. We constucted this database for better understanding of antibiotics regulation. Additilnally, we compair the collected data to similar data in other model organisms showed that the GC content of transcription factor binding sites tends to be correlated with that of the genome whilst that of well-conserved RNA genes such as rRNAs is rather uncorrelated.

FAQ

DBSCR aims to cover all transcriptional regulators of S. coelicolor , or only those described in the literature?
To keep the data quality high, we are collecting transcriptional regulation evens that are validated by wet experiments (literatures).
With the same purpose, we do not have transcriptional regulations that are validated by only genome-wide experiment (e.g. microarray).

What is the difference between "Absolute position" and "Location" in the table?
"Absolute position" shows the position of the motif sequence (transcription factor binding regsion) in the Streptomyces genome (NCBI: AL645882).
"Location" shows relative distance from transcription start site.

What is the abbreviation of exprimental evidences?
Please check this page.

How do you collect the data? (entirely manual scanning of the literature? keyword-based automatic scanning...?)
We are collecting data manually.

Search function

Currently, we proveide the following three search functions from here.

1. Keyword Search
Search for transcription factor or regulated genes with gene name (ex. ahpC, SCO5032).

2. Weight Matrix Search (by sequence)
This search function may help to find transcription factor binding DNA motif in your input promoter sequence. Please enter promoter seqrucne with fasta format or only sequence.

3. Weight Matrix Search (by weight matrix)
This program returns the top 10 similar weight matrices against your input weight matrix.

Use a tab (or space) deliminated format.
The first line, if starting with ">", is ignored.
Both absolute numbers and relative frequencies are acceptable.
Input nucleotides should be in the order A->C->G->T.

Example:

Nucleotide	Position
A	0 0 7 7 7 7 1 6 7 2 0 0 0 0 1
C	0 7 0 0 0 0 0 1 0 0 0 1 0 0 6
G	7 0 0 0 0 0 2 0 0 0 0 0 0 7 0
T	0 0 0 0 0 0 4 0 0 5 7 6 7 0 0

Example format 1:
>RocR
0 0 7 7 7 7 1 6 7 2 0 0 0 0 1
0 7 0 0 0 0 0 1 0 0 0 1 0 0 6
7 0 0 0 0 0 2 0 0 0 0 0 0 7 0
0 0 0 0 0 0 4 0 0 5 7 6 7 0 0

Example format 2:
0 0 1 1 1 1 0.143 0.857 1 0.286 0 0 0 0 0.143
0 1 0 0 0 0 0 0.143 0 0 0 0.143 0 0 0.857
1 0 0 0 0 0 0.286 0 0 0 0 0 0 1 0
0 0 0 0 0 0 0.571 0 0 0.714 1 0.857 1 0 0