<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/37965?offset=120 https://bioinformaticsonline.com/blog/view/43896/list-of-comparative-genomics-resources Tue, 28 Jun 2022 04:08:06 -0500 https://bioinformaticsonline.com/blog/view/43896/list-of-comparative-genomics-resources <![CDATA[List of comparative genomics resources !]]>

Compare structural and functional annotations of proteins between sequenced genomes.

View AREs in the human transcriptome and study the comparative genomics of AREs in model organisms.

Find information about orthologous genes in prokaryotes.

Search for publicly available QTL data on livestocks and animal species.

Find information about bovine genomics data.

A multi-organism web-based resource system designed to easily retrieve, correlate and interpret data across species.

A database resource of developmentally associated conserved non-coding elements.

Delineate conserved non-coding blocks from upstream regions of putative orthologous gene pairs from man, mouse, rat, fugu, Mus musculus, Danio rerio, and zebrafish.

Find coexpressed gene lists and networks in human and mouse.

Construct phylogenetic tree of microorganisms based on oligopeptide content of their complete proteomes.

A novel database server that classifies GenBank's dbEST (database of expressed gene sequences) libraries and removes contaminants.

Find information about the ancestral relationship between genes.

Provides an overview of the genomic organization of microRNAs and extent of conservation during evolution in different metazoan species.

Conduct comparative biometric analysis of chromosomes of different organisms.

Search for Indices of gene and transcripts in human and mouse.

Search and compare 12 new and old Drosophila genomes.

Access to whole genome alignments of human, mouse, rat and fish sequences.

Find eukaryotic paralog/paralogon information.

Analyze the evolutionary process of overlapping genes when comparing different species.

The first publicly available system reported to handle inter-species gene mention normalization.

A web-based software/database system aimed at an improved and accelerated annotation of prokaryotic genomes.

Visualize gene indices of human, mouse, Arabidopsis, Zebrafish, Drosophila and Sheep.

Find information about mutated mouse genes.

A data management and analysis system for metagenomes

Search for influenza sequence, vaccine, and drug resistance information.

LAMHDI, the initiative to Link Animal Models to Human DIsease, is designed to accelerate the research process by providing biomedical researchers with a simple, comprehensive Web-based resource to find the best animal models for their research.

The missing link between multi-species full genome comparisons and functional analysis.

Conduct comparative analysis of completely sequenced microbial genomes.

A biologist-centric software for evolutionary analysis of DNA and protein sequences.

Conduct single nucleotide polymorphisms diversity measurements among homologous sequences from the Mammalia class.

Find information about 1000s of microbial genomes.

A database dedicated to the study of genome conservation.

Explore orthologous relations across 352 complete genomes.

Browse complete genomes in several clades.

A database of orthologous genomic markers for placental mammal phylogenetics.

Conduct genome wide functional and structural analysis.

Conduct genome-wide cis-regulatory module (CRM) predictions for both the human and the mouse genomes.

Compare phenotypes of a given gene or gene set in different model organisms.

Phylemon is a web server that integrates a selected suite of more than 20 different tools from the most popular stand-alone programs of phylogenetic and evolutionary analysis.

Use this database to see where in the evolution some phylogenetic lineages were started, and over which species they were contained.

Search for genomic information on nematode satellite species Pristionchus pacificus.

Find information about related protein sequences.

Database hosting genomics and post-genomics data from multiple protozoans.

A database of pseudogene families based on the protein families from the Pfam database.

Find genomic information about mammals.

Find information about predicted regulons in prokaryotic transcription regulation.

Perform systematic comparison of proteome data among species.

A comparative map viewer dedicated to the biology of the Solanaceae family.

Analyze data from functional analysis on fragmented microbial genetic material.

Visualize and explore comparative genomic hybridization data sets.

Search for genome-wide annotations of regulatory sites in yeast and prokaryotes genomes.

Search for information on adaptive evolution in gene families of higher plants and chordate.

Generate graphical maps of circular genomes that show sequence features, base composition plots, analysis results and sequence similarity plots.

Conduct a comprehensive analysis of genes and genomes.

An interactive online poster presentation on the Macaque genome, including high-quality images, video clips, and Web resources

Search for annotated genetic information of expressed sequence tags (ESTs) in different eukaryotic organisms.

Find mapping and expression information for a unigene cluster (ESTs and full-length mRNA sequences organized into clusters that each represent a unique known or putative gene)

A public online resource for identifying or designing 'universal' overgo-hybridization probes from conserved sequences that can be used to efficiently screen one or more genomic libraries from a designated group of species.

Comprehensive suite of programs and databases for comparative analysis of genomic sequences.

Find metabolic networks and phylogenomic information on a taxonomically diverse range of eukaryotes.

]]> Shruti Paniwala https://bioinformaticsonline.com/blog/view/38248/how-to-set-up-ssh-on-ubuntu-1804 Thu, 22 Nov 2018 10:12:00 -0600 https://bioinformaticsonline.com/blog/view/38248/how-to-set-up-ssh-on-ubuntu-1804 <![CDATA[How to set up SSH on Ubuntu 18.04]]> SSH, also known as Secure Shell or Secure Socket Shell, is a network protocol that gives users, particularly system administrators, a secure way to access a computer over an unsecured network. SSH also refers to the suite of utilities that implement the SSH protocol.

Here are the commands used to connect by Secure SHell:

On the server side

sudo apt-get install ssh

sudo apt-get install openssh-server

sudo /etc/init.d/ssh start

sudo nano /etc/ssh/sshd_config

Uncomment port 22
Uncomment HostKey /etc/ssh/ssh_host_rsa_key
Uncomment AuthorizedKeysFile .ssh/authorized_keys .ssh/authorized_keys2
Set pubkey authentication to "yes"

sudo systemctl restart sshd.service # or sudo /etc/init.d/ssh reload


On the client side:
in ~/.ssh

ssh-keygen -t rsa # set passphrase or not
ssh-copy-id -i ~/.ssh/id_rsa user@100.100.10.100

--> write "yes" then password in


ssh user@100.100.10.100

--> write password --> you should be in

--> in /home/user/.ssh/config type:
Host WhateverName
HostName 100.100.10.100
User username
ForwardX11 yes
ForwardAgent yes
IdentityFile ~/.ssh/id_rsa

--> you should now be able to connect with :

ssh WhateverName

]]> AnHo https://bioinformaticsonline.com/bookmarks/view/41009/genomics-public-data-links Thu, 13 Feb 2020 00:20:00 -0600 https://bioinformaticsonline.com/bookmarks/view/41009/genomics-public-data-links <![CDATA[genomics public data links !]]> List of publically available databases on google server.

More at https://software.broadinstitute.org/gatk/download/bundle

ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/VCF/GATK/.

ftp://ftp.broadinstitute.org/bundle/hg38/hg38bundle/

Address of the bookmark: https://console.cloud.google.com/storage/browser/genomics-public-data/resources/broad/hg38/v0?pli=1

]]> Jit https://bioinformaticsonline.com/bookmarks/view/41901/far-manager-commands-and-links Tue, 23 Jun 2020 06:24:36 -0500 https://bioinformaticsonline.com/bookmarks/view/41901/far-manager-commands-and-links <![CDATA[Far Manager Commands and Links !]]> 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 directories;
  • editing, copying and renaming files;
  • and many other actions.

https://www.farmanager.com/

Basic instruction at

https://conemu.github.io/en/FarManager.html

Plugins at 

https://plugring.farmanager.com/

Address of the bookmark: https://www.farmanager.com/

]]> Jit https://bioinformaticsonline.com/news/view/42324/comparative-genomics-data-set-including-240-mammals-released Thu, 19 Nov 2020 06:45:39 -0600 https://bioinformaticsonline.com/news/view/42324/comparative-genomics-data-set-including-240-mammals-released <![CDATA[Comparative Genomics Data Set Including 240 Mammals Released !]]> The genome of 130 mammals was sequenced by a large international consortium and the data was analyzed together with 110 existing genomes to allow scientists to identify the important positions in the DNA. This report, published in Nature today will help advance research on human disease mutations and inform how best to protect endangered species.

In addition to the knowledge of the human genome, all these genomes, widely sampled across mammals, can be used to research how particular organisms respond to different conditions. Some otters, for example, have a thick, water-resistant shell, and some rodents, but not all, have adapted to hibernation. These animal traits will help us to understand human traits, such as metabolic diseases.

image

With climate change and more animal ecosystems being threatened by human activity, the protection of endangered species is becoming increasingly important. Scientists have historically researched several people in various populations of a species to understand the genetic variation that occurs in that species. This is important for understanding how particular species can be protected. In this study, animals on the Red List of Endangered Species of the International Union for Conservation of Nature had fewer differences in their genomes, which is consistent with their endangered status.

Ref @ A comparative genomics multitool for scientific discovery and conservation https://www.nature.com/articles/s41586-020-2876-6

 Data at http://zoonomiaproject.org/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/35272/biocircosjs-is-an-open-source-interactive-javascript-library-to-interactive-display-biological-data-on-the-web Fri, 19 Jan 2018 15:03:51 -0600 https://bioinformaticsonline.com/bookmarks/view/35272/biocircosjs-is-an-open-source-interactive-javascript-library-to-interactive-display-biological-data-on-the-web <![CDATA[BioCircos.js is an open source interactive Javascript library to interactive display biological data on the web]]> BioCircos.js is an open source interactive Javascript library which provides an easy way to interactive display biological data on the web. It implements a raster-based SVG visualization using the open source Javascript framework jquery.js. BioCircos.js is multiplatform and works in all major internet browsers (Internet Explorer, Mozilla Firefox, Google Chrome, Safari, Opera). Its speed is determined by the client’s hardware and internet browser. For smoothest user experience, we recommend Google Chrome.

BioCircos.js provides SNP, CNV, HEATMAP, LINK, LINE, SCATTER, ARC, TEXT, and HISTGRAMmodules to display genome-wide genetic variations (SNPs, CNVs and chromosome rearrangement), gene expression and biomolecule interactions. BioCircos.js also provides BACKGROUND module to display background and axis circles. Tooltips showing detailed information of SVG elements are also provided.

Demo

Address of the bookmark: http://bioinfo.ibp.ac.cn/biocircos/document/index.html

]]> Jit https://bioinformaticsonline.com/bookmarks/view/38472/gpsrdocker-docker-based-container-that-contain-all-softwareweb-servers-developed-in-the-field-of-bioinformatics Sun, 16 Dec 2018 13:04:46 -0600 https://bioinformaticsonline.com/bookmarks/view/38472/gpsrdocker-docker-based-container-that-contain-all-softwareweb-servers-developed-in-the-field-of-bioinformatics <![CDATA[gpsrdocker: docker-based container that contain all software/web servers developed in the field of bioinformatics.]]> GPSRdocker (http://webs.iiitd.edu.in/gpsrdocker/) is  Presently it contain software developed at G. P. S. Raghava's group (http://webs.iiitd.edu.in/raghava/ ).

The programs and the package are free software for academic users. Permission to use, copy, and modify any part of this software for educational, research and non-profit purposes is hereby granted. In this package or Docker image, number of other supported software has been integrated which may be under other licenses, along with any direct or indirect dependencies of the primary software being contained. As for any pre-built image usage, it is the image user's responsibility to ensure that any use of this image complies with any relevant licenses for all software contained within.

All software packages are distributed in the hope that they will be useful but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. If you have any query, please contact at raghava@iiitd.ac.in.

Address of the bookmark: https://hub.docker.com/r/raghavagps/gpsrdocker/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/41442/gsp4pdb-a-web-tool-to-visualize-search-and-explore-protein-ligand-structural-patterns Sun, 15 Mar 2020 03:41:12 -0500 https://bioinformaticsonline.com/bookmarks/view/41442/gsp4pdb-a-web-tool-to-visualize-search-and-explore-protein-ligand-structural-patterns <![CDATA[GSP4PDB: a web tool to visualize, search and explore protein-ligand structural patterns]]> GSP4PDB is a user-friendly and efficient application to search and discover new patterns of protein-ligand interaction.

GSP4PDB is part of the services provided by the Bioinformatic Group of the University of Talca

http://gdblab.com/gsp4pdb/gsp4pdb2/

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-3352-x

Address of the bookmark: http://gdblab.com/gsp4pdb/gsp4pdb2/

]]> Neel https://bioinformaticsonline.com/bookmarks/view/34812/building-web-uis-with-mojolicious-perl Tue, 26 Dec 2017 18:06:57 -0600 https://bioinformaticsonline.com/bookmarks/view/34812/building-web-uis-with-mojolicious-perl <![CDATA[Building Web UIs With Mojolicious Perl]]> Mojolicious is one of 3 leading web frameworks available in the perl ecosystem (along with Dancer and Catalyst) and by far my favorite.

Mojolicious aims to provide a complete web development experience. It thus has no hard dependencies, comes with a built-in development and production server and many other features one needs to build a web application. It's easy to install, has an applciation generator script and many plugins and extensions.

Libraries for developing Web applications

Address of the bookmark: https://www.ynonperek.com/2017/09/28/perl-mojolicious-web-development/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/26309/ratt Sun, 07 Feb 2016 16:09:40 -0600 https://bioinformaticsonline.com/bookmarks/view/26309/ratt <![CDATA[RATT]]> RATT is software to transfer annotation from a reference (annotated) genome to an unannotated query genome.

It was first developed to transfer annotations between different genome assembly versions. However, it can also transfer annotations between strains and even different species, like Plasmodium chabaudi onto P. berghei, between different Leishmania species or Salmonella enterica onto other Salmonella serotypes. RATT is able to transfer any entries present on a reference sequence, such as the systematic id or an annotator's notes; such information would be lost in a de novo annotation.

More at http://ratt.sourceforge.net/

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

]]> Jitendra Narayan