Address of the bookmark: https://phytozome.jgi.doe.gov/pz/portal.html

http://docpollard.org/

Tools

http://docpollard.org/resources/software/

More at https://www.nature.com/articles/s41467-021-22671-6

Address of the bookmark: https://github.com/dmcblab/InfoGenomeR

• Homology-based misassembly correction
• Homology-based assembly scaffolding and patching
• Scaffold merging

Address of the bookmark: https://github.com/malonge/RagTag

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

Address of the bookmark: https://github.com/PoisonAlien/maftools

USAGE:

• -query: sequence A in fasta format
• -db: sequence B in fasta format
• -out: output matrix
• -kmer Integer: k>1 (default 32) Use 32 for chromosomes and genomes and 16 for small bacteria
• -diffuse Integer: z>0 (default 4) Use 4 for everything - if using large plant genomes you can try using 1
• -dimension Size of the output matrix and plot. Integer: d>0 (default 1000) Use 1000 for everything that is not full genome size, where 2000 is recommended

Address of the bookmark: https://github.com/estebanpw/chromeister

Contact:
Computer Science Building (Science Park 3)
Altenberger Str. 69, A-4040 Linz, Austria
Tel. +43 732 2468 4520 / Fax +43 732 2468 4539
E-mail secretary@bioinf.jku.at

http://www.bioinf.jku.at/

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/

Key Findings of the Study:

1. Alu Insertion and Tail Loss:
   The researchers discovered an Alu-mediated genetic change in a common ancestor of modern apes and humans. This change disrupted the normal function of a gene involved in tail development, leading to the suppression of tail formation.

2. Gene Disruption Mechanism:
   The Alu insertion was found within a regulatory region of the TBXT gene (also known as T or Brachyury), which is crucial for tail development in vertebrates. This insertion likely altered the gene's expression patterns, leading to tail reduction over evolutionary time.

3. Functional Evidence from Model Organisms:
   To test their hypothesis, the researchers introduced similar genetic modifications in mice. The modified mice exhibited shortened or absent tails, supporting the idea that the identified mutation played a role in tail loss in hominoids.

4. Evolutionary Implications:
   The findings suggest that small, random genomic changes—such as transposable element insertions—can have profound effects on body morphology. This study provides evidence that mobile DNA elements (like Alu) can drive major evolutionary transitions.

5. Relevance to Human Evolution:
   Understanding the genetic basis of tail loss helps in reconstructing the evolutionary history of hominins (the lineage that includes humans and our extinct relatives). It also sheds light on how genetic variations contribute to anatomical diversity among primates.

Significance of the Study:

This research highlights the role of transposable elements in shaping evolutionary traits and provides a concrete genetic explanation for a defining characteristic of humans and great apes. It also demonstrates how mutations in regulatory regions of developmental genes can lead to significant anatomical changes.

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/