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Bioinformatics is an interdisciplinary field of science that develops methods and software tools for understanding biological data, especially when the data sets are large and complex. Bioinformatics uses biology, chemistry, physics, computer science, computer programming, information engineering, mathematics and statistics to analyze and interpret biological data. The subsequent process of analyzing and interpreting data is referred to as computational biology.
In bioinformatics, sequence analysis is the process of subjecting a DNA, RNA or peptide sequence to any of a wide range of analytical methods to understand its features, function, structure, or evolution. It can be performed on the entire genome, transcriptome or proteome of an organism, and can also involve only selected segments or regions, like tandem repeats and transposable elements. Methodologies used include sequence alignment, searches against biological databases, and others.
In bioinformatics, sequence clustering algorithms attempt to group biological sequences that are somehow related. The sequences can be either of genomic, "transcriptomic" (ESTs) or protein origin. For proteins, homologous sequences are typically grouped into families. For EST data, clustering is important to group sequences originating from the same gene before the ESTs are assembled to reconstruct the original mRNA.
BioJava is an open-source software project dedicated to provide Java tools to process biological data. BioJava is a set of library functions written in the programming language Java for manipulating sequences, protein structures, file parsers, Common Object Request Broker Architecture (CORBA) interoperability, Distributed Annotation System (DAS), access to AceDB, dynamic programming, and simple statistical routines. BioJava supports a range of data, starting from DNA and protein sequences to the level of 3D protein structures. The BioJava libraries are useful for automating many daily and mundane bioinformatics tasks such as to parsing a Protein Data Bank (PDB) file, interacting with Jmol and many more. This application programming interface (API) provides various file parsers, data models and algorithms to facilitate working with the standard data formats and enables rapid application development and analysis.
Sanger sequencing is a method of DNA sequencing that involves electrophoresis and is based on the random incorporation of chain-terminating dideoxynucleotides by DNA polymerase during in vitro DNA replication. After first being developed by Frederick Sanger and colleagues in 1977, it became the most widely used sequencing method for approximately 40 years. It was first commercialized by Applied Biosystems in 1986. More recently, higher volume Sanger sequencing has been replaced by next generation sequencing methods, especially for large-scale, automated genome analyses. However, the Sanger method remains in wide use for smaller-scale projects and for validation of deep sequencing results. It still has the advantage over short-read sequencing technologies in that it can produce DNA sequence reads of > 500 nucleotides and maintains a very low error rate with accuracies around 99.99%. Sanger sequencing is still actively being used in efforts for public health initiatives such as sequencing the spike protein from SARS-CoV-2 as well as for the surveillance of norovirus outbreaks through the Center for Disease Control and Prevention's (CDC) CaliciNet surveillance network.
Gene structure is the organisation of specialised sequence elements within a gene. Genes contain most of the information necessary for living cells to survive and reproduce. In most organisms, genes are made of DNA, where the particular DNA sequence determines the function of the gene. A gene is transcribed (copied) from DNA into RNA, which can either be non-coding (ncRNA) with a direct function, or an intermediate messenger (mRNA) that is then translated into protein. Each of these steps is controlled by specific sequence elements, or regions, within the gene. Every gene, therefore, requires multiple sequence elements to be functional. This includes the sequence that actually encodes the functional protein or ncRNA, as well as multiple regulatory sequence regions. These regions may be as short as a few base pairs, up to many thousands of base pairs long.
Chitobiosyldiphosphodolichol beta-mannosyltransferase is an enzyme that is encoded by ALG1 whose structure and function has been conserved from lower to higher organisms.
UGENE is computer software for bioinformatics. It works on personal computer operating systems such as Windows, macOS, or Linux. It is released as free and open-source software, under a GNU General Public License (GPL) version 2.
Clone Manager is a commercial bioinformatics software work suite of Sci-Ed, that supports molecular biologists with data management and allows them to perform certain in silico preanalysis.
The Staden Package is computer software, a set of tools for DNA sequence assembly, editing, and sequence analysis. It is open-source software, released under a BSD 3-clause license.
Gene Designer is a computer software package for bioinformatics. It is used by molecular biologists from academia, government, and the pharmaceutical, chemical, agricultural, and biotechnology industries to design, clone, and validate genetic sequences. It is proprietary software, released as freeware needing registration.
In silico PCR refers to computational tools used to calculate theoretical polymerase chain reaction (PCR) results using a given set of primers (probes) to amplify DNA sequences from a sequenced genome or transcriptome.
In metagenomics, binning is the process of grouping reads or contigs and assigning them to individual genome. Binning methods can be based on either compositional features or alignment (similarity), or both.
In bioinformatics, alignment-free sequence analysis approaches to molecular sequence and structure data provide alternatives over alignment-based approaches.
Single nucleotide polymorphism annotation is the process of predicting the effect or function of an individual SNP using SNP annotation tools. In SNP annotation the biological information is extracted, collected and displayed in a clear form amenable to query. SNP functional annotation is typically performed based on the available information on nucleic acid and protein sequences.
Shoba Ranganathan is an Indian Australian biochemist who is a professor of bioinformatics at Macquarie University. Her research considers computational biology and bioinformatics, genome annotation and structural bioinformatics.
References
- ↑ "Home".
- ↑ "Vector NTI". Archived from the original on 2014-12-08. Retrieved 2023-08-11.
- ↑ Tippmann, H.-F. (2004-01-01). "Analysis for free: Comparing programs for sequence analysis". Briefings in Bioinformatics. 5 (1): 82–87. doi: 10.1093/bib/5.1.82 . ISSN 1467-5463. PMID 15153308.
- ↑ Lu, G. (2004-01-01). "Vector NTI, a balanced all-in-one sequence analysis suite". Briefings in Bioinformatics. 5 (4): 378–388. doi: 10.1093/bib/5.4.378 . ISSN 1467-5463. PMID 15606974.
- ↑ "Vector NTI no longer free - Molecular Cloning".
- ↑ "Vector NTI Software - US".
- ↑ "FREQUENTLY ASKED QUESTIONS FOR VECTOR NTI SOFTWARE" (PDF). Retrieved 2023-08-11.
- ↑ Lu, Guoqing; Moriyama, Etsuko (2004). "Vector NTI, a balanced all-in-one sequence analysis suite". Briefings in Bioinformatics. 5 (4): 378–388. doi: 10.1093/bib/5.4.378 . PMID 15606974.