Service package 1: Sequence assembly and annotation
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 SP1 (Sequence assembly and annotation) SYSBIO offers to perform the initial sequence
assembly of bacterial genomes or large DNA fragments, and a semi automated annotation of the
assembled DNA.
Assembly: SYSBIO can perform assembly on sequences produced by 454, Illumina and Sanger
technology. Both assemblies involving reference genomes and de novo assemblies are included
in the service.
Annotation: SYSBIO can perform a semi automated functional annotation of genomes or large
DNA fragments. Both novel genomes and annotation transfer from closely related species are
part of the service.
Table 1 Standard commissioning in SP1 Sequence assembly and annotation
Service
Package (SP)
SP1.a
Task
Assembly:
SP1.b
Gap closure:
SP1.c
Quality control:
SP1.d
Comparative genomics:
SP1.e
Annotation:
Specification
454 technology: Assembly using Newbler (454 Life Sciences).
Illumina technology: Assembly using CASAVA (Illumina).
Other technology: Can be discussed
Both assembly with reference genome and de novo assembly are available.
Mapping against reference: ACT is used to contrast closely related genomes to
aid the correct ordering of contigs.
PCR primers and sequencing reactions: SYSBIO does not have facilities to run
these reactions, but may design suitable primers and assemble new sequence data
when obtained elsewhere.
Both gap closure of paired-end data and single-end data are available
Improve poor quality regions: If complete assembly is available, SYSBIO can
offer to identify regions of the assembly containing poor quality data.
PCR primers and sequencing reactions: SYSBIO does not have facilities to run
these reactions, but may design suitable primers and assemble new sequence data
when obtained elsewhere.
Contrasting closely related DNA sequences: ACT is used to contrast closely
related genomes in order to identify regions of interest. Differences down to single
point mutations can be detected.
Functional annotation: Artemis is used to add biological meaning to DNA
sequences. Depending on the nature of the study, SYSBIO can perform
automatical and manual annotation of DNA sequences
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 1:
Sequence assembly and annotation.

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
Assembly
SP1.b
Gap closure
SP1.c
Quality control
SP1.d
Comparative genomics
SP1.e
Annotation
.
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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Assembly information (to be used for SP1.a)
Details
Information
Project details:
Organism name:
…………………………………………………………
Aim of sequencing:
Base prefect
Draft genome
Other
If other, please specify:
…………………………………………………………
Reference sequencea:
…………………………………………………………
DNA details:
Type of DNA:
Genomic
Plasmid
Viral
Other
If other, please specify:
…………………………………………………………
Size of DNA:
………………..kb
Repetitive sequences:
Technology details:
Sequencing technology:
If other, please specify:
Approximately coverage:
yes
no
unknown
454
Illumina
Other
…………………………………………………………
10 x <
10 – 40 x
> 40 x
Sequencing library details:
Library type:
Paired-end
Fragment size:
………………..bp
Expression systemb:
…………………………………………………………
Single-end
a
If known, please specify with accession number.
Eg. Host or cloning vector.
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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Gap closure information (to be used for SP1.b)
Details
Information
Project details:
Organism name:
…………………………………………………………
Reference sequencea:
DNA details:
Type of DNA:
…………………………………………………………
Genomic
Plasmid
Viral
Other
If other, please specify:
…………………………………………………………
Size of DNA:
………………..kb
Number of contigs:
…………………..
Repetitive sequences:
Technology details:
Sequencing technology:
If other, please specify:
Approximately coverage:
yes
no
unknown
454
Illumina
Other
…………………………………………………………
10 x <
10 – 40 x
> 40 x
Sequencing library details:
Library type:
Paired-end
Fragment size:
………………..bp
Expression systemb:
…………………………………………………………
PCR and sequencing reactionsc:
Single-end
Primer design
Assembly of new sequence reads
a
If known, please specify with accession number.
Eg. Host or cloning vector.
c
SYSBIO does not have facilities to run these reactions, hence must be produced
elsewhere.
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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Quality control (to be used for SP1.c)
Details
Information
Project details:
Organism name:
…………………………………………………………
Reference sequencea:
DNA details:
Type of DNA:
…………………………………………………………
Genomic
Plasmid
Viral
Other
If other, please specify:
…………………………………………………………
Size of DNA:
………………..kb
Repetitive sequences:
Technology details:
Sequencing technology:
If other, please specify:
Approximately coverage:
yes
no
unknown
454
Illumina
Other
…………………………………………………………
10 x <
10 – 40 x
> 40 x
Sequencing library details:
Library type:
Paired-end
Fragment size:
………………..bp
Expression systemb:
…………………………………………………………
Single-end
Assembly detailsc:
Available
PCR and sequencing reactionsd:
Primer design
Assembly of new sequence reads
Not available
a
If known, please specify with accession number.
Eg. Host or cloning vector.
c
Complete assembly, or just the assembled DNA sequence.
d
SYSBIO does not have facilities to run these reactions, hence must be produced
elsewhere.
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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Comparative genomics (to be used for SP1.d)
Details
Information
Project details:
Organism name:
…………………………………………………………
Aim of comparisona:
DNA details:
Type of DNA:
…………………………………………………………
Genomic
Plasmid
Viral
Other
If other, please specify:
…………………………………………………………
Size of DNA:
………………..kb
Repetitive sequences:
Comparison details:
Compare against:
yes
no
unknown
Different species
5 – 20
Different strains
Number of species/strains:
5<
Status of sequencesb:
Complete
Contigs
Annotation of sequencesb:
Available
Not available
> 20
a
Eg. Detection of single point mutations, etc.
The sequences that are to be compared against your sequence.
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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Annotation information (to be used for SP1.e)
Details
Information
Project details:
Organism name:
…………………………………………………………
Aim of annotation:
…………………………………………………………
Reference sequencea:
…………………………………………………………
DNA details:
Type of DNA:
Genomic
Plasmid
Viral
Other
If other, please specify:
…………………………………………………………
Size of DNA:
………………..kb
Repetitive sequences:
Technology details:
Sequencing technology:
If other, please specify:
Approximately coverage:
Annotation details:
Level of accuracy:
Specific annotation:
If other, please specify:
Submission of datab:
yes
no
unknown
454
Illumina
Other
…………………………………………………………
10 – 40 x
10 x <
High
Medium
> 40 x
Low
Homology searches
Protein families
Conserved motifs
Transmembrane helix prediction
N-terminal signal sequence prediction
DNA binding domains
Lipoprotein signal prediction
tRNA prediction
Other
…………………………………………………………
yes
no
a
If known, please specify with accession number.
Submission to public databases such as Genbank
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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