We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.

https://www.science-open.com/document_file/00d79e6c-98e4-425c-9fd1-3a85d5fdefbc/PubMedCentral/00d79e6c-98e4-425c-9fd1-3a85d5fdefbc.pdf

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

J. Appl. Cryst.の発刊に際して

BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.

“Bioinformatics” 특집을 내면서

The Pandoraviridae is a rapidly growing family of giant viruses, all of which have been isolated using laboratory strains of Acanthamoeba. The genomes of ten distinct strains have been fully characterized, reaching up to 2.5 Mb in size. These double-stranded DNA genomes encode the largest of all known viral proteomes and are propagated in oblate virions that are among the largest ever-described (1.2 µm long and 0.5 µm wide). The evolutionary origin of these atypical viruses is the object of numerous speculations. Applying the Chaos Game Representation to the pandoravirus genome sequences, we discovered that the tetranucleotide (4-mer) “AGCT” is totally absent from the genomes of 2 strains (P. dulcis and P. quercus) and strongly underrepresented in others. Given the amazingly low probability of such an observation in the corresponding randomized sequences, we investigated its biological significance through a comprehensive study of the 4-mer compositions of all viral genomes. Our results indicate that “AGCT” was specifically eliminated during the evolution of the Pandoraviridae and that none of the previously proposed host-virus antagonistic relationships could explain this phenomenon. Unlike the three other families of giant viruses (Mimiviridae, Pithoviridae, Molliviridae) infecting the same Acanthamoeba host, the pandoraviruses exhibit a puzzling genomic anomaly suggesting a highly specific DNA editing in response to a new kind of strong evolutionary pressure. Importance The recent years have seen the discovery of several families of giant DNA viruses all infecting the ubiquitous amoebozoa of the genus Acanthamoeba. With dsDNA genomes reaching 2.5 Mb in length packaged in oblate particles the size of a bacterium, the pandoraviruses are the most complex and largest viruses known as of today. In addition to their spectacular dimensions, the pandoraviruses encode the largest proportion of proteins without homolog in other organisms, thought to result from a de novo gene creation process. While using comparative genomics to investigate the evolutionary forces responsible for the emergence of such an unusual giant virus family, we discovered a unique bias in the tetranucleotide composition of the pandoravirus genomes that can only result from an undescribed evolutionary process not encountered in any other microorganism.

https://www.biorxiv.org/content/biorxiv/early/2019/07/23/712018.full.pdf

A spectacular anomaly in the 4-mer composition of the giant pandoravirus genomes reveals a stringent new evolutionary selection process

The numerous whole genome-sequencing projects of the recent genomic era resulted in identifying a huge number of genes with unknown functions, which are now waiting to be characterized. The bioinformatic annotation of prokaryotic genomes, for instance, identifies most of the genes, but leaves 30%–50% of them without any functional attributes [1]. To face this new challenge, many “functional genomics” and “structural genomics” initiatives have been launched throughout the world. One of the goals of structural genomics is to accelerate the discovery of original protein folds as the basis to better understand the protein folding mechanisms, and, thus, improve the performances of computer programs for ab initio 3-D structure modeling or “threading” of proteins. The 3-D structure determination of proteins of known function usually provides detailed insights into their mechanisms of action at the molecular level. It is now expected that the 3-D structure of proteins of unknown function will, in many cases, reveal their similarity to previously described protein families and will immediately provide functional hints that can then be tested experimentally.

Proficient Target Selection in Structural Genomics by In Vitro Protein Expression on Gateway Recombination Plasmids

Megavirus chilensis, a close relative of the Mimivirus giant virus, is able to replicate in Acanthamoeba castellanii. The first step of viral infection involves the internalization of the virions in host vacuoles. It has been experimentally demonstrated that Mimivirus particles contain many proteins capable of resisting oxidative stress, as encountered in the phagocytic process. These proteins are conserved in Megavirus, which has an additional gene (Mg277) encoding a putative superoxide dismutase. The Mg277 ORF product was overexpressed in Escherichia coli, purified and crystallized. A SAD data set was collected to 2.24 A resolution at the selenium peak wavelength on the BM30 beamline at the ESRF from a single crystal of selenomethionine-substituted recombinant superoxide dismutase protein.

Preliminary crystallographic analysis of the Megavirus superoxide dismutase.

/pdf/pithovirus-sibericum-awakening-of-a-giant-virus-of-more-than-4yvxnvu2o8.pdf

[Pithovirus sibericum: awakening of a giant virus of more than 30,000 years].

La saga des virus geants (c’est-a-dire visibles en microscopie optique) a commence il y a plus de 10 ans avec la decouverte de Mimivirus. L’analyse de son genome ADN double brin a revele une complexite genomique equivalente a celle de nombreuses bacteries parasites avec plus d’un millier de proteines differentes participant a son cycle infectieux dans les amibes du [...]

Chantal Abergel

Papers

A spectacular anomaly in the 4-mer composition of the giant pandoravirus genomes reveals a stringent new evolutionary selection process

Proficient Target Selection in Structural Genomics by In Vitro Protein Expression on Gateway Recombination Plasmids

Preliminary crystallographic analysis of the Megavirus superoxide dismutase.

[Pithovirus sibericum: awakening of a giant virus of more than 30,000 years].

Diversité des virus géants