Resources

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.

PacBio Sequel I and Sequel II
We are also running 2 Sequel instruments. 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 1M SMRTcell generates 15Gb of CLR DNA sequence data. An 8M SMRTcell can generate as much as 170Gbases of CLR DNA sequence data. We can run either instrument in CCS or CLR mode. Read lengths very from short to over 100Kb.

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.

Geneious Software
One option to open the DNA sequencing trace files downloaded from our server is to use the software Geneious. Users will need to purchase their own license for the software before they are able to use it. Life Sciences users can send a request to the College of Life Sciences Information Technology (LSIT) and ask that they install Geneious on their computer after receiving the license. For an alternative option 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>.

Other Equipment
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.

Online Resources

BYU Library has also created a resource page of

Sequence Databases

Other DNA Sequencing Facilities

Tools

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).

Database Searching and File Manipulation
EMBL Tools - Database Searching, Browsing and Analysis Tools.
BLAST to FASTA Format - Will convert NCBI BLAST output to FASTA Format.

DNA Tools
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.

Sequence Alignment
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

RNA Tools
mfold - RNA Secondary Structure Prediction.
RNAfold - Predict RNA secondary structure from sequence

Primers & Primer Design
Primer 3 - Picks PCR primers from nucleotide sequences you supply.
OligoCalc - Will calculate the T_M of your oligonucleotides.
Primer Analysis Software - NetPrimer and Beacon Designer free link.

Protein Tools
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).

Miscellaneous
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.

Resources

DNA Sequencing Center Equipment

Online Resources

Tools

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