It takes only a month or two from the discovery of the unreported new coronavirus in December 2019 to the decoding of the genome sequence and registration in a public database.Immediately after the data was released, vaccine development proceeded at an unusual speed.Vaccination began in a short period of about one year, although the supply and system were not yet in place, and as of February 12, 1, the number of vaccinated people in the world exceeded 2 million.
The application of whole-genome information is behind the fact that vaccine development, which would normally take several years, has progressed at such a speed under this pandemic situation.And the foundation that supports them is next-generation sequence technology (NGS).
This time, we will introduce the next-generation sequence analysis PC, which is often inquired about our PC production service "Tegsys", and various software for researching various molecular biology.
table of contents
1. About PC for next-generation sequence analysis
Next-generation sequencerIs a technology for deciphering a base sequence with a huge amount of information, and is characterized by being able to determine multiple DNA sequences at once in parallel.The ability to analyze huge amounts of data faster and more efficiently has led to shorter analysis times and lower costs.In addition, these technologies are useful for various studies such as individual medicine (individualized medicine), hereditary diseases, bacterial flora (saikinso), and microorganisms.
1-1. Consultation on PC specifications
For bioinformatics (next-generation sequencer) PCs that you contact us, memory is generally regarded as important, and depending on the amount of data, it may be necessary to secure storage capacity, but the usage environment and actual The specifications to be selected vary depending on the calculation content and other requests.If you do not know what kind of configuration you should choose, please let us know the software information you plan to use, the processing content you plan to perform, and the calculation scale.If you are considering replacing an existing PC and have any requests or problems such as shortening the analysis processing time or performing a larger calculation, please feel free to contact Tegsys.
|
<Points of consultation>
|
1-2. About existing tools and software
Please let us know the name and version of the tool or software you are using so that we can improve the performance of your PC by checking the software requirements in advance.In particular, the recommended system requirements may differ depending on the software version.
Inquiries We will introduce some of the tools and software that have a proven track record.
|
<Example of the tool you contacted>
|
2. Various software for molecular biology research
With the development of the next-generation sequencer technology mentioned above, the DNA of the sample itself has come to be analyzed and applied from the method of isolating and culturing bacteria from the sample.Genome and transcriptome analyzes for which standard technology has been established have been compiled into a database for use by researchers around the world.
Many of the best software for molecular biology research can take advantage of these databases, and sometimes use multiple databases, so we have many compatible file formats.
2-1. Sequencing / Assembly / Primer Design / Sequence Alignment
■ Clone Manager
For enzyme read management, identical sequence (base sequence) processing, cloning simulation, graphic map drawing, primer design and analysis, global and local sequence alignment, similarity search, laboratory-scale sequence assembly projects Data management and analysis software with a comprehensive set of tools.
Base sequence database:
BLAST (Basic Local Alignment Search Tool) search database can be constructed
(EMBL / Genbank, etc.)
Supported file formats:
GenBank, EMBL, (Can be copied to clipboard in FASTA format)
System requirements:
Windows: 7, 8, 10 (32bit / 64bit compatible)
■ Codon Code Aligner
A program for performing sequence assembly, contig editing, mutation detection, etc. It is compatible with Phred-Phrap and fully supports sequence quality scores.
Base sequence database:
- EMBL (European Molecular Biology Laboratory)
- Genbank
Supported file formats:
SCF, ABI chromatogram, FASTA, FASTQ, GenBank, EMBL, NBRF / PIR, PHD, Plain, SFF, SAM
System requirements:
Windows: XP, Vista, Windows 7, or newer (64bit compatible)
Mac OS X: Requires Mac OS X version 10.7.4 or newer
■ Geneious
It has a simple interface that integrates bioinformatics and molecular biology analysis tools (DNA, RNA, protein sequence alignment and assembly, analysis).
Base sequence database:
NCBI (National Center for Biotechnology Information)… Gene, Genome, Nucleotide, PopSet, Protein, PubMed, SNP, Structure, Taxonomy
Supported file formats:
Supports many file formats including BED, GenBank, Embl / UniProt (import export sequence data)
System requirements:
Windows: 7, 8, 10
Mac OS X: Requires Mac OS X version 10.8 or newer
Linux: CentOS 6 / RHEL6 / Ubuntu Desktop LTS
■ SnapGene
It has functions such as designing and simulating molecular cloning procedures, visualizing those procedures, and automatically creating work history, which helps simplify cloning.You can also convert the created DNA construct into an easy-to-read and easy-to-understand electronic document.
Base sequence database:
VectorNTI Advance or VectorNTI Express * For detailsplease use this form.
Supported file formats:
Supports many file formats including ApE, Embl (ENA), GenBank / DDBJ, Vector NTI ()
System requirements:
Windows: Windows 7, or newer
Mac OS X: Requires Mac OS X version 10.10 or newer
Linux: Ubuntu, Fedra, Ubuntu, Red Hat Enterprise
2-2. Mass spectrometry
■ PREMIER Biosoft
PREMIER Biosoft's highly specialized tools include tools for research, such as mass spectrometry, genomics, mRNA (messenger RNA), proteins, and metabolites.Here is a comprehensive software suite for metabolite data analysisSimMetWill be taken up.
Database:
Humans, E.coli,NIST MS/MSDatabase
Supported file formats:
.txt, .xls, .mzData, .mzXML, Thermo Scientific (* .raw), SCIEX (* .wiff), Bruker Corporation (.baf, .yep, .fid)
System requirements:
Windows: 7, 8, 10 and Vista
■ Protein Metrics
A set of software tools for protein characterization, such as improving routine protein and peptide analysis and streamlining / automating complex workflows.Compatible with any vendor's platform.
Base sequence database:
NCBI (National Center for Biotechnology Information), Byonic (Focused Protein Databases)
Supported file formats:
MGF, mzML, mzXML, or Thermo RAW, FASTA
System requirements:
Windows: 7, 8, 10
Mac OS X: Requires Mac OS X version 10.8 or newer
Linux: CentOS 6 / RHEL6 / Ubuntu Desktop LTS
2-3. Modeling and visualization of metabolic pathways (* reference)
The discipline of the research field in biology is called "research subject + omics", and the comprehensive investigation of the various molecules that make up the living body is called omics analysis (omics, omics).
OmixIs used for interactive mapping of multi-omics data in the direct context of network diagrams, primarily in the areas of transcriptomics, metabolomics, and fluxomics.AlsoCytoscapeIs an open source software platform designed for biological research,Visualize molecular interaction networks and biological pathways.
|
<Omics analysis>
|
■ OmixFeatures (* Reference)
Base sequence database:
KEGG, BioCyc, etc.
Supported file formats:
SBML, SBGM-ML, FluxML, Excel, HDF5, etc.
System requirements:
Windows: 7, 8, 10
Mac OS X: Requires Mac OS X version 10.14 or newer
Linux: Ubuntu 20.04, Fedora 32, openSUSE 15.1, CentOS 8.1 and Manjaro 20. On other Linux distributions and versions you run Omix on your own risk
Resource information for network biology (* reference)
NRNB and Cytoscape
(Introduction to the National Resource for Network Biology)
2-4. Reagent
■ Creative PEG Works
We handle high-purity, high-quality, low-polydispersity, high-reactivity polyethylene glycol (PEG) reagents from Creative PEGWorks..
Click here for a list of PEG products by function, structure and reactivity (Manufacturer page) Can be confirmed
■The molecular biology-related products introduced this time are just a few of our products.
Summary
Bioinformatics is a field related to multiple goals and targets in the SDGs, and is expected to be used in the promotion of Society 5.0 in collaboration with the SDGs.In particular, I think that visualization and utilization of information, from data collection, storage, analysis to integration by sensing technology, will bring about various changes in our lives.We will continue to handle products around the world that are useful for research and development.
Please feel free to contact us for any requests or inquiries such as "I want this software sold by this manufacturer" or "I am having trouble with the analysis speed not increasing".
