BOL: Related items

Flanker

Rahul Nayak — Sat, 27 Feb 2021 22:04:53 -0600

Flanker, a Python package which performs alignment-free clustering of gene flanking sequences in a consistent format, allowing investigation of mobile genetic elements (MGEs) without prior knowledge of their structure. Flanker can be flexibly parameterised to finetune outputs by characterising upstream and downstream regions separately and investigating variable lengths of flanking sequence.

Address of the bookmark: https://github.com/wtmatlock/flanker

GEnView: A phylogeny based comparative genomics software to analyze the genetic environment of genes

Abhi — Tue, 28 Dec 2021 01:49:03 -0600

A phylogeny based comparative genomics software to analyze the genetic environment of genes. The user can select one or several taxa and provide one or several reference protein(s). Genomes and plasmids (based on user choice) will be downloaded from the NCBI Assembly/NR database and searched for the respective gene. Alternatively, custom genomes can be provided. User selected stretches (20kbp by default) of the genes genetic environment are extracted, annotated and aligned between all genomes. The sequences are then visualized, enabling comparison of synteny and gene content.

More at https://pubmed.ncbi.nlm.nih.gov/34951622/

Address of the bookmark: https://github.com/EbmeyerSt/GEnView

33rd Annual Convention of Indian Association for Cancer Research from 13th to 15th February 2014

Tue, 27 Aug 2013 10:37:08 -0500

RGCB is organizing the 33rd Annual Convention of Indian Association for Cancer Research from 13th to 15th February 2014 with the theme "Discovery, Innovation and Translation in Cancer Research"

Kindly log on to conference website http://rgcb.res.in/IACR2014 for further details and timely updates and registration. We shall truly appreciate if the same be circulated among your friends, scholars and students encouraging them to participate in the meet.

http://210.212.237.38/iacrconference/

clusterProfiler

Jit — Thu, 16 Jun 2016 18:57:03 -0500

statistical analysis and visulization of functional profiles for genes and gene clusters

Bioconductor version: Release (3.3)

This package implements methods to analyze and visualize functional profiles (GO and KEGG) of gene and gene clusters.

Author: Guangchuang Yu with contributions from Li-Gen Wang and Giovanni Dall'Olio.

Maintainer: Guangchuang Yu

Citation (from within R, enter citation("clusterProfiler")):

Yu G, Wang L, Han Y and He Q (2012). “clusterProfiler: an R package for comparing biological themes among gene clusters.” OMICS: A Journal of Integrative Biology, 16(5), pp. 284-287.
Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("clusterProfiler")

https://www.bioconductor.org/packages/devel/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html

Address of the bookmark: https://www.bioconductor.org/packages/devel/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html

HybPiper

Jit — Fri, 04 Nov 2016 05:02:10 -0500

HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads.

Targeted bait capture is a technique for sequencing many loci simultaneously based on bait sequences. HybPiper pipeline starts with high-throughput sequencing reads (for example from Illumina MiSeq), and assigns them to target genes using BLASTx or BWA. The reads are distributed to separate directories, where they are assembled separately using SPAdes. The main output is a FASTA file of the (in frame) CDS portion of the sample for each target region, and a separate file with the translated protein sequence.

HybPiper also includes post-processing scripts, run after the main pipeline, to also extract the intronic regions flanking each exon, investigate putative paralogs, and calculate sequencing depth. For more information, please see our wiki.

HybPiper is run separately for each sample (single or paired-end sequence reads). When HybPiper generates sequence files from the reads, it does so in a standardized directory hierarchy. Many of the post-processing scripts rely on this directory hierarchy, so do not modify it after running the initial pipeline. It is a good idea to run the pipeline for each sample from the same directory. You will end up with one directory per run of HybPiper, and some of the later scripts take advantage of this predictable directory structure.

Address of the bookmark: https://github.com/mossmatters/HybPiper

DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies

Shruti Paniwala — Fri, 03 Jan 2020 13:28:19 -0600

DeCoSTAR computes adjacency evolutionary scenarios using a scoring scheme based on a weighted sum of adjacency gains and breakages. Solutions, both optimal and near-optimal, are sampled according to the Boltzmann–Gibbs distribution centered around parsimonious solutions, and statistical supports on ancestral and extant adjacencies are provided. DeCoSTAR supports the features of previously contributed tools that reconstruct ancestral adjacencies, namely DeCo, DeCoLT, ART-DeCo, and DeClone. In a few minutes, DeCoSTAR can reconstruct the evolutionary history of domains inside genes, of gene fusion and fission events, or of gene order along chromosomes, for large data sets including dozens of whole genomes from all kingdoms of life.

Address of the bookmark: https://github.com/YoannAnselmetti/DeCoSTAR_pipeline

Virus 3D Animation

Sat, 26 Oct 2013 09:01:27 -0500

piranha.dl facebook site: http://www.facebook.com/home.php?#!/pages/piranhadl-3D/131721586891915

QuasiModo - Quasispecies Metric Determination on Omics

Neel — Sat, 26 Jun 2021 15:22:56 -0500

This repository contains the scripts and pipeline that reproduces the results of the HCMV benchmarking study. In this study we evaluated genome assemblers and variant callers on 10 in vitro generated, mixed strain HCMV sequence samples, each consisting of two lab strains in different abundance ratios. This tool can also be used to evaluate assemblies and variant calling results on other similar datasets.

https://academic.oup.com/bib/article/22/3/bbaa123/5868070

Address of the bookmark: https://github.com/hzi-bifo/Quasimodo

Mosquito species known for transmitting the Dengue virus

BioStar — Wed, 03 Apr 2024 00:05:51 -0500

Here is a list of mosquito species known for transmitting the Dengue virus along with essential and applied information about each species:

1. Aedes aegypti:
- Geographical Distribution: Found in tropical and subtropical regions worldwide.
- Biting Behavior: Daytime biter, prefers feeding indoors, often around human dwellings.
- Role in Dengue Transmission: Primary vector responsible for transmitting Dengue virus to humans.

2. Aedes albopictus (Asian tiger mosquito):
- Geographical Distribution: Found in tropical, subtropical, and temperate regions worldwide.
- Biting Behavior: Daytime biter, feeds both indoors and outdoors, aggressive feeder.
- Role in Dengue Transmission: Secondary vector, can transmit Dengue virus to humans.

3. Aedes polynesiensis:
- Geographical Distribution: Found in Pacific Islands and coastal regions.
- Biting Behavior: Daytime biter, prefers feeding outdoors, often near coastal areas.
- Role in Dengue Transmission: Vector of Dengue virus in specific geographic regions.

4. Aedes scutellaris:
- Geographical Distribution: Found in Southeast Asia, Pacific Islands, and coastal regions.
- Biting Behavior: Daytime feeder, active in shaded areas, prefers outdoor environments.
- Role in Dengue Transmission: Vector of Dengue virus, particularly in coastal areas.

5. Aedes africanus:
- Geographical Distribution: Found in parts of Africa, including forested areas.
- Biting Behavior: Daytime feeder, prefers shaded areas, bites humans and other animals.
- Role in Dengue Transmission: Vector of Dengue virus in African regions.

Understanding the geographical distribution and biting behavior of these mosquito species is crucial for implementing effective control and prevention strategies to reduce Dengue virus transmission.

Influenza animation - flu virus mechanism

Thu, 17 Oct 2013 19:43:13 -0500

Animation of the mechanism of an influenza virus and how Crucell's antibodies target the HA1 proteins on the virus and prevent further spread of influenza. Client: Crucell Direction, Design & Animation: Daniel Lim, 2Preform Music & Sound Design: Javier Barrero, Logical Disorder Production Company: David Hager, All Terrain Media