DNA Sequencing Center Equipment
Illumina HiSeq 2500
In Rapid Mode generates 125-150Gb of sequence data (2x250) per lane of a 2 lane flow cell, or runs a single flow cell (8 lane flow cell) in “High Output Run Mode” and generates 62.5 Gb of sequence data (2x125) per lane. This machine can operate with twice this capacity in either Rapid Mode (2x2 lanes) or high output mode (2x8 lane). In high output mode it generates some 2 billion reads per flow cell.
We are also running a Sequel instrument. Because the SMRT approach involves sequencing large, intact DNA segments, it dramatically improves or enables several genomics approaches, including: (1) de novo genome assembly, (2) detecting structural variants, (3) constructing full haplotypes, (4) more accurate transcriptome assembly, (5) detecting epigenetic modifications, and (6) direct RNA sequencing to measure post-transcriptional modifications and secondary RNA structure that is lost during cDNA synthesis. Each SMRTcell generates approximately 5Gb of DNA sequence data. Read lengths very from short to over 50Kb.
Applied Biosystems 3730xl DNA Analyzer
In its current configuration, the ABI 3730xl will generate 1,152 (12 x 96) sample reads a day, with each read containing a QV20 read length of approximately 900 bases. This machine can be configured to produce twice as many sample reads a day. For the faster configuration read lengths are shorter with an average QV20 of 650 bases. A second machine is setup for running fragment analysis with either Liz or Rox standards.
BYU users can send a request to the College of Life Sciences Computer Support group and ask that they install Geneious on your computer. This is one option if you are looking for software in which to open the DNA sequencing trace files that you download from our server. There are other software options available (please see below for a link to BioEdit a PC compatible program that is free).
Bioinformatics and Intensive Computation
For the computational aspects of any project, please use the resources of the BYU Fulton Supercomputing Lab, which is already set up with a full suite of bioinformatics and phylogenetic analysis software. The Fulton Supercomputing Lab offers a total of 16,928 CPU cores and about 50 TB of memory across 943 compute nodes. It is supported by approximately 2 petabytes of storage. All nodes have Red Hat Enterprise Linux 6.6. More detail is available at <https://marylou.byu.edu/documentation/resources>.
We have the equipment necessary to prepare and analyze DNA, RNA and the libraries made to run on the equipment we carry. Specifically we have a Fragment Analyzer by Advanced Analytical, an Agilent 2100 Bioanalyzer, a Megaruptor by Diagenode, a Hydroshear, a BluePippin for targeted size selection from Sage Science, a Caliper Gel Chip from PerkinElmer, a Qubit v3.0 Fluorometer, a Coulter Particle Counter, a Tissuelyser, a Turner Biosystems TBS-380 flourometer, and many other small equipment items needed for DNA handling and library preparation.
BYU Library has also created a resource page of
- Genbank Home Page(NCBI)
- Genbank Blast Search
- European Bioinformatics Institute (EBI)
- Japanese GenomeNet
- Swiss Institute of Bioinformatics
- BIOSCI/bionet Electronic Newsgroup Network for Biology
Other DNA Sequencing Facilities
- MSU Research Technology Support Facility
- University of Virginia Health Science Center Sequencing Facility
- Iowa State DNA Facility
- John Hopkins Synthesis & Sequencing Facility
- University of Missouri DNA Core Facility
- University of Utah Health Sciences High Throughput Genomics Facility
Sequence Tools on the Web
Click on the links below in order to access the Sequencing Tools.
The Sequence Manipulation Suite - A collection of 30 different utilities for analyzing and manipulation sequence data.As seen in BioTechniques 28(6): 1102-1104.
A fairly complete list of proteomics tools maintained by ExPASy (Swiss Institute of Bioinformatics).
WebCutter - will produce a restriction map of a sequence you input.
Open Reading Frame Finder - identifies all open reading frames using the standard or alternative codes.
Biological Online Collaboration - multiple users can work together online on biological tasks.
Sanger Institute Software Solutions - many tools for manipulating DNA sequence.
ESPript 3 - Tool to print a multiple alignment.
Multiple Sequence Alignment - At EBI.
Blast - align two sequences using BLAST
LALIGN - find multiple matching subsegments in two sequences
Primers & Primer Design
Primer 3 - Picks PCR primers from nucleotide sequences you supply.
OligoCalc - Will calculate the TM of your oligonucleotides.
Primer Analysis Software - NetPrimer and Beacon Designer free link.
DNA to Protein Translator - Converts DNA sequences to protein sequences.
Peptide Property Calculator - Calculates Molecular Weight, Length of the Peptide, and Others.
Protein Calculator - Will calculate Molecular Weight, Charge, UV Absorbtion, Atom and Residue Counts, and Solvent Content.
PredictProtein - Prediction of transmembrane helix location and topology (Columbia University).
Centrifuge Helper - Helps to calculate g-values for various centrifuge models and rotors.
FreeWare Sequence Editing Software: (Download and install on your machine). Note: Please DO NOT install these software packages on DNASC computers. There are many free programs available that can open .ab1 files, such as 4Peaks(Mac), SnapGene Viewer(Mac/PC), FinchTV(Mac/PC), Sequence Scanner(PC), and Chromas(PC).
Sequence Analysis Software
ClustalW2 - Multiple Sequence Alignment Program.
PHYLIP v3.57 - by Joe Felsenstein.
PAUP* v4.0 - by David Swofford.
TFPGA - Tools for Population Genetic Analyses, by Mark Miller.