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) / Task / SpecificationSP1.a / Assembly: / 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.
SP1.b / Gap closure: / 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
SP1.c / Quality control: / 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.
SP1.d / Comparative genomics: / 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.
SP1.e / Annotation: / 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
Preliminary order form Service package 1:
Sequence assembly and annotation.
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 / Assembly
SP1.b / Gap closure
SP1.c / Quality control / .
SP1.d / Comparative genomics
SP1.e / Annotation
Assembly information (to be used for SP1.a)
Project details:
Organism name:
Aim of sequencing:
If other, please specify:
Reference sequencea: / …………………………………………………………
Base prefect Draft genome Other
…………………………………………………………
…………………………………………………………
DNA details:
Type of DNA:
If other, please specify:
Size of DNA:
Repetitive sequences: / Genomic Plasmid Viral Other
…………………………………………………………
………………..kb
yes no unknown
Technology details:
Sequencing technology:
If other, please specify:
Approximately coverage: / 454 Illumina Other
…………………………………………………………
10 x < 10 – 40 x > 40 x
Sequencing library details:
Library type:
Fragment size:
Expression systemb: / Paired-end Single-end
………………..bp
…………………………………………………………
aIf known, please specify with accession number.
bEg. Host or cloning vector.
Gap closure information (to be used for SP1.b)
Project details:
Organism name:
Reference sequencea: / …………………………………………………………
…………………………………………………………
DNA details:
Type of DNA:
If other, please specify:
Size of DNA:
Number of contigs:
Repetitive sequences: / Genomic Plasmid Viral Other
…………………………………………………………
………………..kb
…………………..
yes no unknown
Technology details:
Sequencing technology:
If other, please specify:
Approximately coverage: / 454 Illumina Other
…………………………………………………………
10 x < 10 – 40 x > 40 x
Sequencing library details:
Library type:
Fragment size:
Expression systemb: / Paired-end Single-end
………………..bp
…………………………………………………………
PCR and sequencing reactionsc: / Primer design
Assembly of new sequence reads
aIf known, please specify with accession number.
bEg. Host or cloning vector.
cSYSBIO does not have facilities to run these reactions, hence must be produced elsewhere.
Quality control (to be used for SP1.c)
Project details:
Organism name:
Reference sequencea: / …………………………………………………………
…………………………………………………………
DNA details:
Type of DNA:
If other, please specify:
Size of DNA:
Repetitive sequences: / Genomic Plasmid Viral Other
…………………………………………………………
………………..kb
yes no unknown
Technology details:
Sequencing technology:
If other, please specify:
Approximately coverage: / 454 Illumina Other
…………………………………………………………
10 x < 10 – 40 x > 40 x
Sequencing library details:
Library type:
Fragment size:
Expression systemb: / Paired-end Single-end
………………..bp
…………………………………………………………
Assembly detailsc: / Available Not available
PCR and sequencing reactionsd: / Primer design
Assembly of new sequence reads
aIf known, please specify with accession number.
bEg. Host or cloning vector.
cComplete assembly, or just the assembled DNA sequence.
dSYSBIO does not have facilities to run these reactions, hence must be produced elsewhere.
Comparative genomics (to be used for SP1.d)
Project details:
Organism name:
Aim of comparisona: / …………………………………………………………
…………………………………………………………
DNA details:
Type of DNA:
If other, please specify:
Size of DNA:
Repetitive sequences: / Genomic Plasmid Viral Other
…………………………………………………………
………………..kb
yes no unknown
Comparison details:
Compare against:
Number of species/strains:
Status of sequencesb:
Annotation of sequencesb: / Different species Different strains
5 < 5 – 20 > 20
Complete Contigs
Available Not available
aEg. Detection of single point mutations, etc.
bThe sequences that are to be compared against your sequence.
Annotation information (to be used for SP1.e)
Project details:
Organism name:
Aim of annotation:
Reference sequencea: / …………………………………………………………
…………………………………………………………
…………………………………………………………
DNA details:
Type of DNA:
If other, please specify:
Size of DNA:
Repetitive sequences: / Genomic Plasmid Viral Other
…………………………………………………………
………………..kb
yes no unknown
Technology details:
Sequencing technology:
If other, please specify:
Approximately coverage: / 454 Illumina Other
…………………………………………………………
10 x < 10 – 40 x > 40 x
Annotation details:
Level of accuracy:
Specific annotation:
If other, please specify: / High Medium Low
Homology searches
Protein families
Conserved motifs
Transmembrane helix prediction
N-terminal signal sequence prediction
DNA binding domains
Lipoprotein signal prediction
tRNA prediction
Other
…………………………………………………………
Submission of datab: / yes no
aIf known, please specify with accession number.
bSubmission to public databases such as Genbank
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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