BOL: Related items

Visualise blast results !

Abhi — Tue, 11 Oct 2022 03:15:10 -0500

Kablammo helps you create interactive visualizations of BLAST results from your web browser. Find your most interesting alignments, list detailed parameters for each, and export a publication-ready vector image, all without installing any software.

Address of the bookmark: https://kablammo.wasmuthlab.org/

KOALA: KEGG's internal annotation tool for K number assignment of KEGG GENES using SSEARCH computation

Abhimanyu Singh — Wed, 12 Dec 2018 09:16:55 -0600

KOALA (KEGG Orthology And Links Annotation) is KEGG's internal annotation tool for K number assignment of KEGG GENES using SSEARCH computation. BlastKOALA and GhostKOALA assign K numbers to the user's sequence data by BLAST and GHOSTX searches, respectively, against a nonredundant set of KEGG GENES. Annotate Sequence in KEGG Mapper and Pathogen Checker in KEGG Pathogen are special interfaces to the BlastKOALA server and can be executed in an interactive mode. See Step-by-step Instructions.

Reference: Kanehisa, M., Sato, Y., and Morishima, K. (2016) BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J. Mol. Biol. 428, 726-731. [pubmed] [pdf]

Address of the bookmark: https://www.kegg.jp/blastkoala/

Linux operating system aimed at scientists

Pranjali Yadav — Mon, 19 Jan 2015 08:30:49 -0600

The Bio-Linux operating system is based on Ubuntu 14.04 LTS (Trusty Tahr), and the previous version was using Ubuntu 12.04 LTS. The developers only use LTS releases and that means that upgrades for this distro don't come along all that often.

This Linux distribution is aimed at scientists and it comes with more than 250 bioinformatics packages, 50 graphical applications and several hundred command line tools. And this is just skimming the surface of what the OS can do. Users have access to even more apps from the official repositories.

Bio-Linux is using an Ubuntu LTS version as its base

The fact that it uses Ubuntu LTS versions for the base is a good thing because it means its users won't have to worry about the support. Ubuntu 14.04 LTS is supported until 2019, so people who are using Bio-Linux shouldn't have a problem.

"An updated Bio-Linux 8 version is now on the website in ISO and OVA versions. As usual, there is no need to download this version if you are an existing user. All updates to existing packages will be applied to your system through the update manager and new packages are all available via apt-get or Synaptic," reads the announcement.

The changelog also states that a problem that was preventing the desktop to not start on VirtualBox has been fixed, the QIIME and Bowtie-Bio tools have been upgraded, the pandaseq paired end assembler has been added, and the beginners tutorial specific to Bio-Linux 8 has been improved.

Check out the official announcement for a complete list of changes and updates. You can download Bio-Linux 8.0.5 right now from Softpedia and give it a spin. It has the Unity desktop and now it runs very well in virtual environments.

Reference @ http://news.softpedia.com/news/Bioinformatics-Distro-Bio-Linux-8-0-5-Now-Available-for-Download-469867.shtml

AMR Database !

LEGE — Tue, 04 Jun 2024 13:37:21 -0500

ARG-ANNOT. PMID: 24145532
CARD. PMID: 23650175
MEGARes PMID: 27899569
NCBI BioProject: PRJNA313047
plasmidfinder PMID: 24777092
resfinder. PMID: 22782487
VFDB. PMID: 26578559
SRST2's version of ARG-ANNOT. PMID: 25422674.
VirulenceFinder PMID: 24574290.

Address of the bookmark: https://github.com/sanger-pathogens/ariba/wiki/Task%3A-getref

ncbi-datasets-cli -- Quickstart: command line tools !

Jit — Tue, 07 Dec 2021 02:51:26 -0600

Install and use the NCBI Datasets command line tools

The NCBI Datasets datasets command line tools are datasets and dataformat .

Use datasets to download biological sequence data across all domains of life from NCBI.

Use dataformat to convert metadata from JSON Lines format to other formats.

Conda download:

https://anaconda.org/conda-forge/ncbi-datasets-cli

Buld Download

https://www.ncbi.nlm.nih.gov/datasets/builder/?tax_id=29979

Address of the bookmark: https://www.ncbi.nlm.nih.gov/datasets/docs/v1/quickstarts/command-line-tools/

repeat-aware: Repeat aware scaffolding evaluation framework by Igor Mandric

Jit — Wed, 21 Mar 2018 18:10:00 -0500

Genome scaffolding is a classical challenging problem in bioinformatics. It refers to joining assembly contigs into chains (called scaffolds). The join between two contigs A and B is considered correct if:

Their relative orientation is correct
Their relative order is correct
The gap estimate is similar to the true distance on the reference

The problem of scaffolding validation is also a challenging one. One of the main issues which hinders from an adequate scaffolding evaluation are genome repeats. The previous standard for evaluation (Hunt et al., Genome Biology, 2014) did not take into account repeats. In this evaluation framework, repeats are taken into account.

The new evaluation framework considers the optimal assignment of contigs in the output scaffolding to contigs in the reference scaffolding in the sense of the number of correct links.

https://github.com/mandricigor/repeat-aware

Address of the bookmark: https://github.com/mandricigor/repeat-aware

Bioinformatics 101 - Running BLAST

Tue, 03 Sep 2013 14:59:50 -0500

How to format the database for BLAST, run the command, view the output file, and use BioPerl and Perl to parse the output. By David Francis, Ohio State University. Delivered live at the Tomato Disease Workshop 2010. For more information, please visit http://www.extension.org/pages/32521/bioinformatics-101-video.

BLAST

Wed, 25 Sep 2013 10:56:23 -0500

Dr. Rob Edwards describes how BLAST works

BRIG

Jit — Thu, 16 Feb 2017 13:14:25 -0600

BRIG is a free cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data. The application is available at:http://sourceforge.net/projects/brig

If you have any questions or comments, post them on one of the trackers on BRIG’s SourceForge page:http://sourceforge.net/tracker/?group_id=328245.

Features:

Images show similarity between a central reference sequence and other sequences as concentric rings.
BRIG will perform all BLAST comparisons and file parsing automatically via a simple GUI.
Contig boundaries and read coverage can be displayed for draft genomes; customized graphs and annotations can be displayed.
Using a user-defined set of genes as input, BRIG can display gene presence, absence, truncation or sequence variation in a set of complete genomes, draft genomes or even raw, unassembled sequence data.
BRIG also accepts SAM-formatted read-mapping files enabling genomic regions present in unassembled sequence data from multiple samples to be compared simultaneously

Address of the bookmark: http://brig.sourceforge.net/

New Layout for BLAST ftp Database Site

Jit — Tue, 21 Jan 2020 11:57:11 -0600

As announced previously, the new default database version for BLAST+ is dbV5. To complete this transition, the ftp database site will be updated to support this change. We expect this change to happen around February 4^th, please adjust your scripts or procedures accordingly.

Here is a list of what is changing:

All databases at the root level will be dbV5.
The dbV5 file naming, “_v5” will be removed. Databases with no “_vX” descriptor will be dbV5.
dbV4 tarballs will be renamed with "_v4", files included in tarball will not be renamed.
dbV4 databases will be moved to a v4 subdirectory.
As of 1/13/20 the Cloud directory will be frozen with no more new entries.
The will be no more updates to dbV4 databases.
The FASTA directory will contain nr, nt, swissprot, and pdbaa files.

If you have any questions or concerns, please contact blast-help@ncbi.nlm.nih.gov