Service package 2: DNA sequence analysis
The bioinformatics platform in integrated system biology (SYSBIO) offers three service packages:
SP1: Sequence assembly and annotation
SP2: DNA sequence analysis
SP3: Mapping of biological data
In SP2 (DNA sequence analysis) SYSBIO offers to perform computational prediction of various
features in bacterial genomes or large DNA fragments. This includes prediction of small RNAs,
promoters and Rho independent terminators, and transcription factor bindings sites. It is also
possible to request other form of sequence analysis.
Transcription factor bindings sites: Because of the nature of these genes and features, it is
crucial that we can base our analysis on data that have been obtained experimentally.
Small RNA: SYSBIO combine several methodologies to predict these genes. This includes the
prediction of promoters and terminators, and comparative genomics.
Table 1 Standard commissioning in SP2 DNA sequence analysis
Service
Package (SP)
SP2.a
Task
Promoter prediction:
Specification
Sigma factors: If -10 and -35 binding motifs are known and conserved or organism
closely related to e. coli, SYSBIO may perform prediction of different sigma factors.
Search matrices are built from known binding sites and genomes (or other DNA)
are scanned for similar motifs.
SP2.b
Terminator prediction:
Rho independent terminators: Genomes (or other DNA) are scanned for Rho
independent terminators.
SP2.c
Transcription factor
binding site prediction:
Conserved binding motifs: If information of transcription factor binding sites from
an organism (or family) is known, SYSBIO may perform prediction similar binding
sites throughout whole genomes (or other DNA).
Other conserved motifs: Can be discussed
SP2.d
Small RNA prediction:
Advanced gene prediction: Prediction of small regulatory RNA will combine the
above methods and include comparative genomic (conservation between species).
Also folding energy is taken into account in the prediction.
sRNA target prediction: Can be discussed
Platform of Integrated System Biology
University of Tromsø, N-9037 Tromsø, Telephone: (+47) 77 64 40 00, Fax (+47) 77 64 47 65
Direct telephone: (+47) 77 62 33 72, E-mail: sysbio@ik.uit.no
http://uit.no/sysbio
Preliminary order form Service package 2:
DNA sequence analysis.

Please place tick marks to indicate which tasks are desired. For simplicity this icon
can be
copied and replaced by the empty boxes. Then return this electronic form by E-mail to SYSBIO,
and you will receive in response a tailored order form and prizes for placing the final order.
Order:
Date:
…../…../20……
Title:
Customer:
Institution:
Address:
Contact person 1:
E-mail:
Phone:
Contact person 2:
E-mail:
Phone:
Order:
(Tick)
SP
Task
SP1.a
Promoter prediction
SP1.b
Terminator prediction
SP1.c
Transcription factor binding site prediction
SP1.d
Small RNA prediction
.
Platform of Integrated System Biology
University of Tromsø, N-9037 Tromsø, Telephone: (+47) 77 64 40 00, Fax (+47) 77 64 47 65
Direct telephone: (+47) 77 62 33 72, E-mail: sysbio@ik.uit.no
http://uit.no/sysbio
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Service package 2 (to be used for SP2.a-d)
Details
Information
Project details:
Organism name:
…………………………………………………………
………………..kb
Size of DNA:
Promoter prediction:
yes
Type of sigma factor:
Terminator prediction:
Information about terminatorsa:
Transcription factor binding sites:
Transcription factor:
Information about transcription
factor binding siteb:
σ70
no
σ54
yes
no
yes
no
yes
no
σ32
σ28
σ24
σ19
…………………………………………………………
yes
no
yes
no
RNA sequencing data:
yes
no
Experimentally verified small
RNAc:
yes
no
Small RNA:
σ38
a
If known, please inform SYSBIO upon request.
Please provide SYSBIO any known information about the particular binding site.
c
Please provide SYSBIO any known information about known small RNAs.
b
Platform of Integrated System Biology
University of Tromsø, N-9037 Tromsø, Telephone: (+47) 77 64 40 00, Fax (+47) 77 64 47 65
Direct telephone: (+47) 77 62 33 72, E-mail: sysbio@ik.uit.no
http://uit.no/sysbio
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