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This Month in Bioinformatics- Research Updates of May 2021

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This Month in Bioinformatics- Research Updates of May 2021

In this article, we summarize the latest interesting findings made this month in bioinformatics.

1. A new software for detection and quantification of genome editing translocation from NGS data

New software called CRISPECTOR is developed for accurate estimation of genome editing translocation and off-target activity from NGS data [1]. It performs statistical analysis of NGS data from multiplex-PCR comparative experiments. Later, it quantifies the translocation events. CRISPECTOR is a command-line tool that is available as a Bioconda package at http://bioconda.github.io/recipes/crispector/README.html. The source can be found at GitHub.

For more information, read here.

2. A new suite to model cis-regulatory elements for motif occurrence combinatorics

A newly expanded suite is developed to model the motif occurrence combinatorics in DNA sequences [2]. This suite is known as MOCCA (Motif Occurrence Combinatorics Algorithms). It is based on support vector machines (SVM) and random forest (RF) models, SVM-MOCCA and RF-MOCCA respectively. MOCCA is implemented in C++ with a minimal number of dependencies to ease the process of installation. It can be installed on Unix-based systems.

For more information, read here.

3. An updated version of IPD to analyze the SARS-CoV-2 genome

IPD2.0 [3] is an updated version of the Infectious Pathogen Detector (IPD) [4] is developed. It helps in deriving insights from the SARS-CoV-2 genome. IPD is a computational pipeline that consists of an analysis module of SARS-CoV-2. This module performs genomic analysis that helps in understanding the dynamics and variability of the virus. The SARS-CoV-2 module generates SARS-CoV-2 genomic samples and works on phylogenetic clade analysis. It is written in Python3 and the desktop version is available for Linux requiring Conda and Tkinter for its installation.

For more information, read here.

4. Novel tool to discover DNA motifs associated with CpG methylation events

A new tool called CpGmotifs is developed to find DNA motifs associated with CpG methylation events [5]. CpGmotifs is based on short DNA motif discovery. it retrieves and characterizes DNA patterns related to CpG methylation in the human genome. It is written in R language and comes with an easy GUI. The source code is freely accessible on GitHub along with a docker image available on DockerHub.

For more information, read here.

5. A novel method to accurately prioritize cancer-driving genes

A novel method called driveR is developed to accurately prioritize cancer-driving genes using somatic genomics data [6]. It is based on batch analysis that prioritizes the driver genes using somatic genomics data. The driveR has been tested on 28 datasets and provides the most accurate results as compared to the other standard methods. This package is written in R and is platform-independent. The driveR is freely accessible on CRAN.

For more information, read here.

6. A new tool for manual refinement of 3D microscopy annotations

A new open-source tool called Segmentor is developed that allows manual annotation and refinement of objects from 3D microscopy annotations [7]. It is based on a 2D-3D approach to visualize and segment objects within the 3D image. Segmentor is developed in C++ and is available for Windows, Mac, and Linux. It is freely accessible for non-academic use and is available at https://www.nucleininja.org/ and https://github.com/RENCI/Segmentor.

For more information, read here.


References

  1. Amit, I., Iancu, O., Levy-Jurgenson, A. et al. (2021). CRISPECTOR provides accurate estimation of genome editing translocation and off-target activity from comparative NGS data. Nat Commun 12, 3042.
  2. Bredesen, B.A., Rehmsmeier, M. (2021). MOCCA: a flexible suite for modelling DNA sequence motif occurrence combinatorics. BMC Bioinformatics 22, 234.
  3. Desai, S., Rane, A., Joshi, A. et al. (2021). IPD 2.0: To derive insights from an evolving SARS-CoV-2 genome. BMC Bioinformatics 22, 247.
  4. Desai, S., Rashmi, S., Rane, A., Dharavath, B., Sawant, A., & Dutt, A. (2021). An integrated approach to determine the abundance, mutation rate and phylogeny of the SARS-CoV-2 genome. Briefings in bioinformatics22(2), 1065-1075.
  5. Scala, G., Federico, A. & Greco, D. (2021). CpGmotifs: a tool to discover DNA motifs associated to CpG methylation events. BMC Bioinformatics 22, 278.
  6. Ülgen, E., Sezerman, O.U. (2021). driveR: a novel method for prioritizing cancer driver genes using somatic genomics data. BMC Bioinformatics 22, 263.
  7. Borland, D., McCormick, C.M., Patel, N.K. et al. Segmentor: a tool for manual refinement of 3D microscopy annotations. BMC Bioinformatics 22, 260 (2021).

Bioinformatics News

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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What is mane project?

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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This Month in Bioinformatics- Research Updates of March 2022

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This Month in Bioinformatics- Research Updates of March 2022

Here are the latest research developments in the field of bioinformatics made in the month of March 2022. (more…)

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This month in Bioinformatics- Research Updates of November 2021

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This month in Bioinformatics- Research Updates of November 2021

We summarize the latest research published this month in the field of bioinformatics. (more…)

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This Month in Bioinformatics- Research Updates of October 2021

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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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This Month in Bioinformatics- Research Updates of June 2021

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This Month in Bioinformatics- Research Updates of June 2021

In this article, we summarize the latest interesting findings made this month of June in bioinformatics. (more…)

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This Month in Bioinformatics- Research Updates of April 2021

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This Month in Bioinformatics- Research Updates of April 2021

In this article, we summarize the latest interesting findings made this month in bioinformatics. (more…)

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This Month in Bioinformatics- Research Updates of March 2021

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Bioinformatics Monthly Research Updates- March 2021

Here, we summarize the latest interesting findings made this month in bioinformatics. (more…)

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This Month in Bioinformatics- Research Updates of February 2021

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Monthly Research Updates- February 2021

We summarize the research done in bioinformatics in the month of February. (more…)

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This Month in Bioinformatics- Research Updates of January 2021

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This month in Bioinformatics- January 2021

In this article, we summarize the main findings made in bioinformatics this month. (more…)

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This Month in Bioinformatics- Research Updates of December 2020

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This Month in Bioinformatics- Research Updates of December 2020

In this article, we summarize the latest research in bioinformatics published this month. (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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This Month in Bioinformatics- Research Updates of November 2020

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In this article, we summarize the latest research in bioinformatics published this month. (more…)

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This Month in Bioinformatics- Research Updates of October 2020

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Some of the important findings made this month in bioinformatics are mentioned in this article. (more…)

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This Month in Bioinformatics: Research Updates of September 2020

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Bioinformatics Monthly updates- September 2020

Some of the important findings made this month in bioinformatics are mentioned in this article. (more…)

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This Month in Bioinformatics: Research Updates of August 2020

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Bioinformatics Research Updates- August 2020

Some of the important findings made this month in bioinformatics are mentioned in this article. (more…)

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This month in Bioinformatics: Research Updates of July 2020

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Some of the important findings made this month in bioinformatics are mentioned in this article. (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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A workshop on Genome Editing Tools and Techniques

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Department of Biotechnology (DBT), India is organizing a 5-day workshop on CRISPR/Cas mediated genome editing in plants: Applications, tools, and experimental design” to address the strategies and methods involved in genome modification utilized as essential tools in research and development. (more…)

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