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This Month in Bioinformatics- Research Updates of November 2020

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Research updates of bioinformatics- November 2020

In this article, we summarize the latest research in bioinformatics published this month.

1. No increased SARS-CoV-2 transmission due to recurrent mutations

Recently, Dorp et al., [1] have tested whether SARS-CoV-2 transmission is increasing due to the recurrent mutations. To check this, they have created a phylogenetic index. This index quantifies the relative number of descendants in sister clades with and without a specific allele [1]. They collected 46,723 SARS-CoV-2 genomes isolated from covid19 patients worldwide and applied this index to the dataset. The current mutations appeared to be evolutionarily neutral. For more information, read here.

2. A new tool for transcriptomic data analysis

A new tool called GIANT-Galaxy-based tool for Interactive ANalysis of Transcriptomic data has been developed by Vandel et al., [2]. GIANT is a set of tools allowing researchers to analyze transcriptomic data from microarray or RNA-seq analyses [2]. It consists of different modules facilitating the easy selection of tools for a particular analysis. The source code of the GIANT is freely downloadable on Github (https://github.com/juliechevalier/GIANT). The Galaxy tool suite is available on the Galaxy Main Tool Shed (https://toolshed.g2.bx.psu.edu; name:suite_giant; owner:vandelj). For more information, read here.

3. New tool for marker set selection and genomic prediction

A new tool called GMStool is developed. This tool is based on Genome-wide Association Studies (GWAS) and uses statistical and machine-learning methods [3]. GMStool is written in R and is available at www.github.com/JaeYoonKim72/GMStool. It shows higher performance than the other available tools. For more information, read here.

4. A new database about the regulatory relationship between human papillomavirus and host RNA

HRRD is a new manually curated database that contains the regulatory relationship between human papillomavirus and host RNA [4]. The host RNA includes mRNA, miRNA, and lncRNA. The information for this database is obtained from 10,761 papers in Pubmed. The database is easily accessible at www.hmuhrrd.com/HRRD. For more information, read here.

5. A New Protein-Protein Interaction Network Aligner

AligNet is a new protein-protein interaction network aligner based on a parameter-free pairwise alignment algorithm [5]. It provides biologically and topologically efficient alignments. AligNet algorithm focuses on structural matching and protein function conservation. It is implemented in the R language and is freely available to download from GitHub.


References

  1. van Dorp, L., Richard, D., Tan, C. C., Shaw, L. P., Acman, M., & Balloux, F. (2020). No evidence for increased transmissibility from recurrent mutations in SARS-CoV-2. bioRxiv.
  2. Vandel, J., Gheeraert, C., Staels, B., Eeckhoute, J., Lefebvre, P., & Dubois-Chevalier, J. (2020). GIANT: Galaxy-based tool for Interactive ANalysis of Transcriptomic data. Scientific Reports.
  3. Jeong, S., Kim, J. Y., & Kim, N. (2020). GMStool: GWAS-based marker selection tool for genomic prediction from genomic data. Scientific reports10(1), 1-12.
  4. Yan, B., Zhang, S., Yu, S., Hussain, S., Liu, T., Wang, B., … & Wei, L. (2020). HRRD: a manually-curated database about the regulatory relationship between HPV and host RNA. Scientific Reports10(1), 1-5.
  5. Alcalá, A., Alberich, R., Llabrés, M., Rosselló, F., & Valiente, G. (2020). AligNet: alignment of protein-protein interaction networks. BMC bioinformatics21(6), 1-22.

Bioinformatics News

VS_Analysis: A Python package to perform post-virtual screening analysis

Dr. Muniba Faiza

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VS_Analysis: A Python package to perform post-virtual screening analysis

Virtual screening (VS) is a crucial aspect of bioinformatics. As you may already know, there are various tools available for this purpose, including both paid and freely accessible options such as Autodock Vina. Conducting virtual screening with Autodock Vina requires less effort than analyzing its results. However, the analysis process can be challenging due to the large number of output files generated. To address this, we offer a comprehensive Python package designed to automate the analysis of virtual screening results.

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Proteins shape analyses reveal novel forms and connections.

Dr. Muniba Faiza

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Protein shape analyses reveal novel forms and connections.

A new study has revealed new forms of proteins that have never been seen before along with unexpected connections. Last year, Google DeepMind predicted the structure of all known proteins from organisms using AlphaFold [1].

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What is MANE project?

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MANE is a collaborative project between NCBI and EMBL-EBI. It stands for Matched Annotation from NCBI and EMBL-EBI [1]. The datasets provided by NCBI and EMBL-EBI on the human genome are not identical across every gene.

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BLAST+ 2.12.0- A more efficient version of BLAST is available

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A new more efficient version of BLAST+ 2.12.o is available now [1]. This version provides more efficient multithreaded searches. (more…)

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Join Bioinformatics Review Research Group

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We are going to lead a few bioinformatics research projects. For that, we are creating a new research group of Bioinformatics Review. (more…)

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Inviting Nominations for ‘Top 5 Bioinformaticians in India 2020’

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Bioinformaticians Awards

Bioinformatics Review compiles a list of top bioinformaticians every two years. We are inviting nominations for the second edition of this award after the 2018 List. We invite you to contribute to this endeavor by nominating your colleague or friends if you think they can make it to our list.

Nominations start from 20th June 2020 till 15th August 2020. All the nominees will be informed via email on 5th September 2020. We use a well-established ranking method called ScipRank. Our data collection is open-source. ScipRank methodology is publicly available for scrutiny.

Also, we are completing 5th year of success in Bioinformatics Review this year. On this occasion, we are organizing an International Conference on Advanced Research in Bioinformatics 2020. The award will be declared at the conclusion of ConARB 2020 –  3 & 4th Oct 2020).

We invite you to contribute to this endeavor by nominating your colleague or friends. You can also submit your papers, which if accepted, can be presented at the conference.

We have set up a dedicated portal for ConARB 2020 accessible here https://conarb.bioinformaticsreview.com.
To attend or to submit your abstract or to nominate someone, kindly visit this website. Accepted papers will be published in a special issue of Bioinformatics Review.

We are looking forward to your continued support, contributions, nominations, and suggestions for the conference as well as your active participation.

 

 

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