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|  University of Hawai'i Manoa |
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| University of Hawai'i Manoa |
The ASGPB genome infrastructure currently consists of several state-of-the-art capillary-based DNA sequencers and accessory equipment to deal with large sample volumes. The facility can process up to 9000 samples per day with a projected sequence output of 6.75 Million bases. Several prokaryotic and one eukaryotic genome project are currently in progress.
The facility offers DNA sequencing services for a wide range of templates including plasmid DNA, PCR fragments, cosmid DNA, and Bacterial Artificial Chromosomes (BACs). Sequencing reactions are performed using Applied Biosystems BigDye terminator chemistry and are run on ABI 3730XL capillary-based DNA sequencers.
Member:
Hou, Shaobin, Ph.D.
Role:
Associate Researcher
"The 96-capillary 3730xl DNA Analyzer is the Gold Standard for high throughput genetic analysis. Use this for DNA fragment analysis applications such as microsatellites, AFLP, SNP analysis, mutation detection and traditional DNA sequencing. Get the highest quality data at a low cost per sample." This facility has 6 capillary-based sequencers.
"The 96-well GeneAmp PCR System 9700 contains two sample blocks, each of which holds a maximum of 96 sample wells. Fully loaded, the instrument accommodates up to 192 samples per run. The system can also be used with a single 96-well plate for smaller runs."
This lab has 2 ABI GeneAmp 9700 thermal cyclers.
"Offering more than 1 million high-quality reads per run and read lengths of 400 bases, the system is ideally suited for de novo sequencing of whole genomes and transcriptomes of any size, metagenomic characterization of complex samples, resequencing studies and more."
Service uses Eppendorff kits or the overnight high-throughput template preparation via the Rolling Circle Amplification (RCA) method.
"The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families."
""EMBOSS is "The European Molecular Biology Open Software Suite". EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole. EMBOSS breaks the historical trend towards commercial software packages."
"Multiple alignment of nucleic acid and protein sequences."
"Hmmpfam reads a sequence file seqfile and compares each sequence in it, one at a time, against all the HMMs in hmmfile looking for significantly similar sequence matches. "