ABI 3130xl genetic analyzer information
The facility DNA sequencing system was upgraded in January 2008 from the ABI 3100 to the ABI 3130xl. Following is some information on the system:
- General ABI 3130xl information: Applied Biosystems 3130 and 3130xl Genetic Analyzers: One Polymer, One Capillary Array Length, Maximum Performance (Applied Biosystems application note)
- Microsatellite analysis on the ABI 3130xl: Microsatellite Analysis on the Applied Biosystems
3130 Series Genetic Analyzers (Applied Biosystems fact sheet)
- Sequencing reaction protocol for BigDye: BigDye Terminator v3.1 Cycle Sequencing Kit Protocol (Applied Biosystems protocol)
- Methylated DNA sequencing protocol: Methylation Analysis by Bisulfite Sequencing: Chemistry, Products and Protocols from Applied Biosystems (Applied Biosystems protocol)
- Methylated DNA sequencing protocol: methylSEQr System: Bisulfite Conversion
and Sequencing of Methylated DNA (Applied Biosystems protocol summary)
Recommended DNA purification kits
- Qiagen DNA purification kits
- Other purification kits may be suitable—please contact the facility to discuss
Notes on analysis of results with sequence analysis software V5.3
- KB basecaller V1.1:
- A novel basecaller algorithm that performs basecalling for pure and mixed base calls.
- Generation of quality values (QV) to provide basecall accuracy information for pure and mixed base calls.
- QV = -10 log10 (Pe)Where Pe is the probability of error
- The KB basecaller generates QVs from 1 to 99, and the QVs are optionally displayed as bars above each base in the Sequences and Electropherograms views.
QV Bar color Significance 0 to 14 Red Not acceptable 15 to 19 Yellow Need manual review 20 Blue Acceptable
- Clear range is the region of a DNA sequence that remains after excluding the low quality or error-prone sequence at both 5’and 3’ ends. The data excluded from the clear range is shown in gray.
- Multiple formats of output sequence files:
- Analyzed ABI files (.ab1)
- Text file in ABI or Fasta (.seq)
- Phred (.phd.1) files
- Standard chromatogram format (.scf) files
- Acrobat (.pdf)
Generally we provide ABI and Fasta files, but if clients require other type of the sequence files, we can re-analyze data, and then send phred or chromatogram files.
Software for sequence file analysis
- Finch TV to view, edit, print, and blast your sequence data.
- ApE-A Plasmid Editor, to view, edit, and analyze data, including alignment of multiple sequences.
- Sequence Scanner from ABI to edit and view both analyzed and raw sequence data, clear range at 5’ and 3’ ends, QVs and QV bars for the sequences, and export traces in multiple formats including pdf, phd.1, seq etc.
If you have any suggestions for additions or edits to this page, please contact the facility.
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