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Primer Analysis Software - NetPrimer and Beacon Designer free link.ĭNA to Protein Translator - Converts DNA sequences to protein sequences. OligoCalc - Will calculate the T M of your oligonucleotides. Primer 3 - Picks PCR primers from nucleotide sequences you supply.

RNAfold - Predict RNA secondary structure from sequence Mfold - RNA Secondary Structure Prediction. LALIGN - find multiple matching subsegments in two sequences Sanger Institute Software Solutions - many tools for manipulating DNA sequence.ĮSPript 3 - Tool to print a multiple alignment. Open Reading Frame Finder - identifies all open reading frames using the standard or alternative codes.īiological Online Collaboration - multiple users can work together online on biological tasks.

WebCutter - will produce a restriction map of a sequence you input. The Sequence Manipulation Suite - A collection of 30 different utilities for analyzing and manipulation sequence data.As seen in BioTechniques 28(6): 1102-1104.Ī fairly complete list of proteomics tools maintained by ExPASy (Swiss Institute of Bioinformatics).ĮMBL Tools - Database Searching, Browsing and Analysis Tools.īLAST to FASTA Format - Will convert NCBI BLAST output to FASTA Format.

University of Utah Health Sciences High Throughput Genomics FacilityĬlick on the links below in order to access the Sequencing Tools.

University of Missouri DNA Core Facility.

John Hopkins Synthesis & Sequencing Facility.

University of Virginia Health Science Center Sequencing Facility.

MSU Research Technology Support Facility.

BIOSCI/bionet Electronic Newsgroup Network for Biology.

European Bioinformatics Institute (EBI).

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.īYU Library has also created a resource page of We have the equipment necessary to prepare and analyze DNA, RNA and the libraries made to run on the equipment we carry. All nodes have Red Hat Enterprise Linux 6.6. It is supported by approximately 2 petabytes of storage. The Fulton Supercomputing Lab offers a total of 16,928 CPU cores and about 50 TB of memory across 943 compute nodes.

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There are other software options available (please see below for a link to BioEdit a PC compatible program that is free).įor 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.

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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.

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A second machine is setup for running fragment analysis with either Liz or Rox standards.īYU users can send a request to the College of Life Sciences Computer Support group and ask that they install Geneious on your computer. For the faster configuration read lengths are shorter with an average QV20 of 650 bases. This machine can be configured to produce twice as many sample reads a day. 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. Read lengths very from short to over 100Kb. We can run either instrument in CCS or CLR mode. An 8M SMRTcell can generate as much as 170Gbases of CLR DNA sequence data. Each 1M SMRTcell generates 15Gb of CLR DNA sequence data. 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. We are also running 2 Sequel instruments. In high output mode it generates some 2 billion reads per flow cell. This machine can operate with twice this capacity in either Rapid Mode (2x2 lanes) or high output mode (2x8 lane). 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.

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