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- Jit@jit.aber
Jit posted a new ad in the Opportunity Senior Scientist (Bioinformatics/ IT) at Regional Centre for Biotechnology 1606 days ago
- Jit@jit.aber
Jit posted to the wire 1606 days ago

Bioinformatics scientist at RCB https://www.rcb.res.in/upload/Advt_IBDC_FINAL.pdf #RCB #Bioinformatics
- Jit@jit.aber
Jit bookmarked Liftoff: an accurate tool that maps annotations in GFF or GTF between assemblies 1606 days ago

Liftoff, an accurate tool that maps annotations in GFF or GTF between assemblies of the same, or closely-related species. Unlike current coordinate lift-over tools which require a pre-generated “chain” file as input, Liftoff is a...

https://github.com/agshumate/Liftoff
- Jit@jit.aber
Jit bookmarked PhiSpy: PhiSpy identifies prophages in Bacterial (and probably Archaeal) genomes 1606 days ago

PhiSpy identifies prophages in Bacterial (and probably Archaeal) genomes. Given an annotated genome it will use several approaches to identify the most likely prophage regions. Initial versions of PhiSpy were written by Sajia Akhter...

https://github.com/linsalrob/PhiSpy
- Jit@jit.aber
Jit bookmarked truvari: Structural variant comparison tool for VCFs 1606 days ago

Structural variant comparison tool for VCFs Given benchmark and comparsion sets of SVs, calculate the recall, precision, and f-measure. Spiral Genetics Motivation

https://github.com/spiralgenetics/truvari
- BioStar@biostar
BioStar posted to the wire 1609 days ago

Unpicking the complexity of DNA mutations https://www.ebi.ac.uk/about/news/announcements/DNA-lesions #DNA #Mutation
- BioStar@biostar
BioStar bookmarked The wavefront alignment (WFA) algorithm 1609 days ago

The wavefront alignment (WFA) algorithm is an exact gap-affine algorithm that takes advantage ofhomologous regions between the sequences to accelerate the alignment process. As opposed to traditional dynamic programming algorithms that run in...

https://github.com/smarco/WFA
- Jit@jit.aber
Jit commented on the blog Tools to detect synteny blocks regions among multiple genomes 1613 days ago

halSynteny program makes it possible to speed up the computations by over two times in comparison with SatsumaSynteny2, another popular tool. Such high efficiency was attained by implementing a mathematically effective algorithm using...
- Shruti Paniwala@shruti
Shruti Paniwala posted a new ad in the Opportunity Research Associate Bioinformatics in IISc Recruitment 2020 1613 days ago
- Jit@jit.aber
Jit commented on a bookmark Far Manager Commands and Links ! 1614 days ago

alt-f1 to switch between directories and server netbox shift-f4 to add new session
- Jit@jit.aber
Jit bookmarked Far Manager Commands and Links ! 1614 days ago

Far Manager is a program for managing files and archives in Windows operating systems. Far Manager works in text mode and provides a simple and intuitive interface for performing most of the necessary actions: viewing files and...

https://www.farmanager.com/
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- Jit@jit.aber
  
  Jit 1142 days ago
  Just F1 commands
  
  F1- show / hide the left panel
  
  F2- show / hide right panel
  
  F3- sort by file name
  
  F4- sort by extension
  
  F5- sort by recording time
  
  F6- sort by size
  
  F7- do not sort
  
  F8- sort by creation time
  
  F9- sort by access time
  
  F10- sort by description
  
  F11- sort by file owner
  
  F12- start sorting menu
- Jit@jit.aber
  
  Jit 1142 days ago
  You can also open an additional menu by holding down the button Shift, which is mainly intended for working with files and archives, namely:
  
  F1- add files to archive
  
  F2- extract files from archive
  
  F3- execute archive management commands
  
  F4- edit new file
  
  F5- copy the file under the cursor
  
  F6- rename or move the file under the cursor
  
  F7- absent
  
  F8- delete the file under the cursor
  
  F9- save configuration
  
  F10- select the last executed menu item
  
  F11- use sorting about groups
  
  F12- show marked files first
- Jit@jit.aber
  
  Jit 1142 days ago
  We press the combination Alt keys+ F1 or Alt + F2, in the menu that opens, select NetBox, it is under the number 2.
  Now we need to create a connection to our server. Let's say you have data for connecting via SSH:
  Login: root, password: pass, server IP: 127.0.0.1, port 22
  As suggested to create a new session, press Shift + F4 and enter the data:
+3 more
- Jit@jit.aber
Jit posted a new ad in the Opportunity Stay-at-Home RevBayes Workshop 1617 days ago
- Jit@jit.aber
Jit bookmarked KAD: Assessing genome assemblies using K-mer copies in assemblies and K-mer abundance in Illumina... 1618 days ago

KAD is designed for evaluating the accuracy of nucleotide base quality of genome assemblies. Briefly, abundance of k-mers are quantified for both sequencing reads and assembly sequences. Comparison of the two values results in a single value per...

https://github.com/liu3zhenlab/KAD
- Jit@jit.aber
Jit bookmarked sunbeam: A robust, extensible metagenomics pipeline 1619 days ago

Sunbeam is a pipeline written in snakemake that simplifies and automates many of the steps in metagenomic sequencing analysis. It uses conda to manage dependencies, so it doesn't have pre-existing dependencies or admin...

https://github.com/sunbeam-labs/sunbeam
- Jit@jit.aber
Jit posted to the wire 1619 days ago

New #phased #genome #assembly revealed, scandalous #rotifers have #homologous #chromosomes ! https://www.biorxiv.org/content/10.1101/2020.06.16.155473v1
- Shruti Paniwala@shruti
Shruti Paniwala bookmarked Coronavirus SARS-CoV-2 1620 days ago

Used Nanographics Vj, our real-time molecular visualization and animation software, to create this video showing the structure of the virus. In the video, you can see the latest theory on how the RNA is organized inside of the virus particle. On...

https://nanographics.at/projects/sars-cov-2/
- Neel@neelam
Neel commented on the news BLAST+ updated !!! 1621 days ago

Latest blast at https://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/
- Neel@neelam
Neel bookmarked HDOCK SERVER 1621 days ago

HDOCK SERVER Protein-protein and protein-DNA/RNA docking based on a hybrid algorithm of template-based modeling and ab initio free docking. The HDOCK server distinguishes itself from similar docking servers in its ability to support...

http://hdock.phys.hust.edu.cn/
- BioStar@biostar
BioStar commented on a bookmark AutoDock Vina: an open-source program for doing molecular docking. 1624 days ago

AutoDockFR (or ADFR in short) is a protein-ligand docking program developed in the Sanner laboratory at Scripps Research under the AutoDock umbrella. https://ccsb.scripps.edu/adfr/
- BioStar@biostar
BioStar commented on a bookmark AutoDock Vina: an open-source program for doing molecular docking. 1624 days ago

QVina-W, a new docking tool particularly useful for wide search space, especially for blind docking. QVina-W utilizes the powerful scoring function of AutoDock Vina, the accelerated search of QVina 2, and adds thorough search for wide search...

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