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• • BioStar@biostar

  

  BioStar bookmarked The wavefront alignment (WFA) algorithm 1653 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 1657 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 1657 days ago
• • Jit@jit.aber

  

  Jit commented on a bookmark Far Manager Commands and Links ! 1658 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 ! 1658 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/

  Comments

  • • Jit@jit.aber

    

    Jit 1186 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 1186 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 1186 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 1661 days ago
• • Jit@jit.aber

  

  Jit bookmarked KAD: Assessing genome assemblies using K-mer copies in assemblies and K-mer abundance in Illumina... 1662 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 1663 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 1663 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 1664 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 !!! 1665 days ago

  Latest blast at https://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/
• • Neel@neelam

  

  Neel bookmarked HDOCK SERVER 1665 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. 1668 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. 1668 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...
• • BioStar@biostar

  

  BioStar bookmarked VirtualFlow: a versatile, parallel workflow platform for carrying out virtual screening 1668 days ago

   related tasks on Linux-based computer clusters of any type and size which are managed by a batchsystem (such as SLURM).  Currently, there exist two versions of VirtualFlow, which are tailored to different types of tasks: VFLP:...

  https://virtual-flow.org/
• • BioStar@biostar

  

  BioStar bookmarked AutoDock Vina: an open-source program for doing molecular docking. 1668 days ago

  AutoDock Vina is an open-source program for doing molecular docking. It was designed and implemented by Dr. Oleg Trott in the Molecular Graphics Lab at The Scripps Research Institute. It is especially effective for protein-ligand...

  http://vina.scripps.edu/

  Comments

  • • BioStar@biostar

    

    BioStar 1668 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 space. 

    https://qvina.github.io/

  • • BioStar@biostar

    

    BioStar 1668 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/
• • Jit@jit.aber

  

  Jit bookmarked HS3D: Homo Sapiens Splice Sites Dataset 1669 days ago

  HS3D (Homo Sapiens Splice Sites Dataset) is a data set of Homo Sapiens Exon, Intron and Splice regions extracted from GenBank Rel.123. The aim of this data set is to give standardized material to train and to assess the prediction accuracy of...

  http://www.sci.unisannio.it/docenti/rampone/
• • Neel@neelam

  

  Neel posted to the wire 1669 days ago

  Beginner’s guide to #comparative #bacterial #genome analysis using next-generation sequence data https://microbialinformaticsj.biomedcentral.com/articles/10.1186/2042-5783-3-2
• • Jit@jit.aber

  

  Jit bookmarked PPAI: a web server for predicting protein-aptamer interactions 1669 days ago

  PPAI can query aptamers and proteins, predict aptamers and predict protein-aptamer interactions in batch mode precisely and efficiently, which would be a novel bioinformatics tool for the research of protein-aptamer interactions. PPAI web-server is...

  http://39.96.85.9/PPAI/
• • Jit@jit.aber

  

  Jit commented on a bookmark Coronavirus Resources ! 1669 days ago

  Gene and protein expression data of human genes implicated in the virus infection of the host cells. Identifying cell types and genes with highest expression in SARS-CoV-2 infections. https://www.covid19dataportal.org/expression?db=expression

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