DNA Sequencing Center Equipment

454 Life Sciences Genome Sequencer
    This machine is set up for Titanium runs, which means there should be 2 millions raw wells on the two halves of a plate. It is expected that sequence information from some 2/3 of these wells will pass the quality filters. If all goes well during a run, the median read length should be around 450 bases. In such a situation we can return more than 500 million bases of DNA sequence information. This machine can also be configured to run the older FLX plates which don't have as high a capacity.

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.

Applied Biosystems 3100 Genetic Analyzer
    The ABI 3100 is currently configured to run fragment analysis (not DNA sequencing). It can handle 460 samples a day in its current configuration.

Parallab 350
    The Parallab 350 aspirates small and accurate reagent volumes, performs the thermal cycling, and subsequently completes all of the purification steps within the proprietary Nano-Pipetter which is comprised of 96 miniature glass tubes working simultaneously.  Each reagent is aspirated into the tubes, mixed, thermal cycled and purified before finally being dispensed into an output plate for analysis.  After each sample set is completed, the Nano-Pipetter is cleaned and reused.

Genetix QPix2XT   
    Picks a defined number of clones from a tray or dish. Cherry picks subclones with 100% accuracy into microwell plates using an integrated plate management system. Can also be used to put Arrays onto nylon membranes.

Sequencher Software
    BYU users can send a request to the College of Life Sciences Computer Support group and ask that they install Sequencher on your MAC 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).



Links to Online Resources

BYU Library has also created a resource page of

• Molecular Biology Subject Page

Sequence Databases

• Genbank Home Page(NCBI)
• Genbank Blast Search
• EMBL Sequence Database
• European Bioinformatics Institute (EBI)
• Japanese GenomeNet
• Australian National Genomic Information Service (ANGIS)
• ISREC bioinformatics group
• BIOSCI/bionet Electronic Newsgroup Network for Biology
• EMBnet

Other DNA Sequencing Facilities

• MSU DNA Sequencing Facility Homepage
• University of Virginia Health Science Center Sequencing Facility
• Joslin Diabetes Center Core Sequencing Facility
• Iowa State University DNA Sequence and Synthesis Facility -- This site has a great DNA sequencing troubleshooting guide 
• John Hopkins Sequencing Facility
• Molecular Biology Program DNA Core Facility at the University of Missouri, Columbia.
• San Diego State University Sequencing Facility
• University of Utah Health Sciences DNA Sequencing Facility

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
Seq Reverse - Will reverse compliment any sequence.
ReadSeq - (Baylor College of Medicine) - Several useful utilities.
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.
BackTranslate - translate a protein sequence into a nucleotide sequence, using any desired codon usage table.
BackTranslate - maintained by the University at Buffalo, The State University of New York.
GeneWise2 - compares a protein sequence to a genomic DNA sequence.
SEQERR - detection of frameshift error in coding regions

Sequence Alignment
ESPript - Tool to print a multiple alignment.
Clustal W - At EBI.
ALIGN - 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 Design - NetPrimer and Beacon Designer free link.

Protein Tools
DNA to Protein Translator - Converts DNA sequences to protein sequences.
Protein Alignment Coloring Tool - Will color protein alignments based on hydrophobicity of the amino acids.
Peptide Property Calculator - Calculates Molecular Weight, Length of the Peptide, and Others.
ProtCalc - 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, use Sequencher instead.
MacOS - EditView 1.0.1 - by Applied Biosystems.
Windows 95/NT4.0 or higher - Chromas 2.32 A minimal cost software for handling trace files.
Win95/98/NT/2K/XP - BioEdit - Biological Sequence Alignment Editor. (Freeware)

Sequence Analysis Software:
ClustalX - 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.