BOL: Abhi's bookmarks

genomenotebook

Abhi — Thu, 20 Apr 2023 13:19:01 -0500

https://dbikard.github.io/genomenotebook/

Install

pip install genomenotebook

How to use

Create a simple genome browser with a search bar. The sequence appears when zooming in.

import genomenotebook as gn

g=gn.GenomeBrowser(genome_path, gff_path, init_pos=10000)
g.show()

Tracks can be added to visualize your favorite genomics data. See Examples for more !!!!

Address of the bookmark: https://dbikard.github.io/genomenotebook/

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/

Covid Spectrum !

Abhi — Sun, 25 Sep 2022 18:58:14 -0500

https://cov-spectrum.org/explore/World/AllSamples/

CoV-Spectrum supports a wide range of search queries. The following sections presents search options of the basic search bar. For information on the advanced search

Address of the bookmark: https://cov-spectrum.org/

Covid Spectrum !

Abhi — Sun, 25 Sep 2022 18:57:50 -0500

https://cov-spectrum.org/explore/World/AllSamples/

CoV-Spectrum supports a wide range of search queries. The following sections presents search options of the basic search bar. For information on the advanced search

Address of the bookmark: https://cov-spectrum.org/

Covid Spectrum !

Abhi — Sun, 25 Sep 2022 18:56:47 -0500

https://cov-spectrum.org/explore/World/AllSamples/

Address of the bookmark: https://cov-spectrum.org/

Executing Snakemake

Abhi — Sun, 25 Sep 2022 18:34:30 -0500

This part of the documentation describes the snakemake executable. Snakemake is primarily a command-line tool, so the snakemake executable is the primary way to execute, debug, and visualize workflows.

https://github.com/snakemake/snakemake/blob/main/docs/tutorial/basics.rst

Address of the bookmark: https://snakemake.readthedocs.io/en/v4.5.1/executable.html

gfastats: The swiss army knife for genome assembly.

Abhi — Thu, 08 Sep 2022 06:03:05 -0500

gfastats is a single fast and exhaustive tool for summary statistics and simultaneous *fa* (fasta, fastq, gfa [.gz]) genome assembly file manipulation. gfastats also allows seamless fasta<>fastq<>gfa[.gz] conversion. It has been tested in genomes even >100Gbp.

Address of the bookmark: https://github.com/vgl-hub/gfastats

Elastic BLAST !

Abhi — Tue, 06 Sep 2022 18:14:57 -0500

ElasticBLAST is a new way to BLAST large numbers of queries, faster and on the cloud. Here are the top three reasons you should use ElasticBLAST:

1. ElasticBLAST can handle much LARGER queries!

ElasticBLAST can search query sets that have hundreds to millions of sequences and against BLAST databases of all sizes.

2. ElasticBLAST is FASTER

ElasticBLAST distributes your searches across multiple cloud instances to process them simultaneously. The ability to scale resources in this way allows you to process large numbers of queries in a shorter time than you could with BLAST+.

3. ElasticBLAST is EASY to run on the cloud

ElasticBLAST is easy to set up using our step-by-step instructions (Amazon Web Services (AWS), Google Cloud Platform (GCP)) and allows you to leverage the power of the cloud. Once configured, it manages the software and database installation, handles partitioning of the BLAST workload among the various instances, and deallocates cloud resources when the searches are done.

ElasticBLAST also selects the instance (i.e., machine) type for you based on database size. Of course, you can also choose the instance type manually if you prefer.

Address of the bookmark: https://blast.ncbi.nlm.nih.gov/doc/elastic-blast/

oGNM:Conformational dynamics based on contact topology in a coarse-grained presentation

Abhi — Mon, 17 Jan 2022 03:52:51 -0600

Gaussian Network Model (GNM) is a powerful tool to sample conformational dynamics based on contact topology in a coarse-grained presentation. Here we present a method to consider protein dynamics in the presence of ‘environment’ (1). The ‘environment’ here can be crystal contacts defined in structures solved by x-ray crystallography, a protein in homo-/hetero-dimers, a part of a protein complex, the DNA in complexed with transcription factors, or even a large ligand (or ligands) in a protein. The protein dynamics, in the presence of these ‘environments’, can be assessed in a more rigorous physics ground (the size and number of the orthogonal normal modes are the same as those in unperturbed systems (in the absence of the environment)) with our theories (2) that guarantee our implementations to be more efficient (saving 3/4 time, assuming equal size of system and environment), more memory friendly (saving >1/2 time) and more accurate (enhanced correlation between predictions and B-factors). The environment consideration in ANM theory was published (1) and reviewed (2); its GNM counterpart is first derived in this work and proven to be more accurate in the B-factor predictions than conventional GNM.

Address of the bookmark: https://dyn.life.nthu.edu.tw/oGNM/oGNM.php

MimiLook: A Phylogenetic Workflow for Detection of Gene Acquisition in Major Orthologous Groups of Megavirales

Abhi — Mon, 10 Jan 2022 06:32:22 -0600

This tool detects statistically validated events of gene acquisitions with the help of the T-REX algorithm by comparing individual gene tree with NCBI species tree. In between the steps, the workflow decides about handling paralogs, filtering outputs, identifying Megavirale specific OGs, detection of HGTs, along with retrieval of information about those OGs that are monophyletic with organisms from cellular domains of life.

https://www.readcube.com/articles/10.3390%2Fv9040072

Address of the bookmark: https://pubmed.ncbi.nlm.nih.gov/28387730/