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) / Task / SpecificationSP2.a / Promoter prediction: / 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
Preliminary order form Service package 2:
DNA sequence analysis.
Please place tick marks to indicate which tasks are desired. For simplicity this icon Q 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: (TickQ) / SP / Task
SP1.a / Promoter prediction
SP1.b / Terminator prediction
SP1.c / Transcription factor binding site prediction / .
SP1.d / Small RNA prediction
Service package 2 (to be used for SP2.a-d)
Project details:
Organism name:
Size of DNA: / …………………………………………………………
………………..kb
Promoter prediction:
Type of sigma factor: / yes no
σ70 σ54 σ38 σ32 σ28 σ24 σ19
Terminator prediction:
Information about terminatorsa: / yes no
yes no
Transcription factor binding sites:
Transcription factor:
Information about transcription factor binding siteb: / yes no
…………………………………………………………
yes no
Small RNA:
RNA sequencing data:
Experimentally verified small RNAc: / yes no
yes no
yes no
aIf known, please inform SYSBIO upon request.
bPlease provide SYSBIO any known information about the particular binding site.
cPlease provide SYSBIO any known information about known small RNAs.
Platform of Integrated System Biology
University of Tromsø, N-9037 Tromsø, Telephone: (+47) 77 64 40 00, Fax (+47) 77 64 4765
Direct telephone: (+47) 77 62 33 72, E-mail:
http://uit.no/sysbio
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