<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/41863?offset=70 https://bioinformaticsonline.com/bookmarks/view/44882/fantasia Wed, 20 Aug 2025 02:48:15 -0500 https://bioinformaticsonline.com/bookmarks/view/44882/fantasia <![CDATA[FANTASIA]]> FANTASIA is an advanced pipeline for the automatic functional annotation of protein sequences using state-of-the-art protein language models. It integrates deep learning embeddings and in-memory similarity searches, retrieving reference vectors from a PostgreSQL database with pgvector, to associate Gene Ontology (GO) terms with proteins.

https://www.nature.com/articles/s42003-025-08651-2

Address of the bookmark: https://github.com/CBBIO/FANTASIA

]]> BioStar https://bioinformaticsonline.com/blog/view/11592/xampp-starting-apache-fail-ubuntu Sat, 07 Jun 2014 05:52:35 -0500 https://bioinformaticsonline.com/blog/view/11592/xampp-starting-apache-fail-ubuntu <![CDATA[XAMPP: Starting Apache fail Ubuntu]]> Once you install XAMMP on linux, the most common problem you face is Apache failure. To fix the issues please use following command to first stop and then again start it.

sudo /etc/init.d/apache2 stop

sudo /etc/init.d/mysql stop

sudo /etc/init.d/proftpd stop

sudo /opt/lampp/lampp start

 

PhpMyAdmin “Wrong permissions on configuration file, should not be world writable!”

Once the Xammp is installed, it might be possible to set up the configuration file in writable mode. Try the following steps:

Just chmod 0755 the file

sudo chmod 0755 config.inc.php
]]> Ram Yash Pal https://bioinformaticsonline.com/bookmarks/view/23892/bioinformatics-made-easy-search-bioinformatics-tools-and-run-genomic-analysis-in-the-cloud Thu, 20 Aug 2015 02:21:20 -0500 https://bioinformaticsonline.com/bookmarks/view/23892/bioinformatics-made-easy-search-bioinformatics-tools-and-run-genomic-analysis-in-the-cloud <![CDATA[Bioinformatics Made Easy Search: Bioinformatics tools and run genomic analysis in the cloud]]> InsideDNA makes hundreds of bioinformatics tools immediately available to run via an easy-to-use web interface and allows an accurate search across all functions, tools and pipelines.

With InsideDNA, you can upload and store your own genomic/genetic datasets in a limitless cloud space, and instantly analyze it with a powerful compute instance, without any tool installation or set up hassle.

More at https://insidedna.me/

Address of the bookmark: https://insidedna.me/

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/38378/gwaspro-a-high-performance-genome-wide-association-analysis-server Fri, 07 Dec 2018 08:04:57 -0600 https://bioinformaticsonline.com/bookmarks/view/38378/gwaspro-a-high-performance-genome-wide-association-analysis-server <![CDATA[GWASpro: A High-Performance Genome-Wide Association Analysis Server]]> GWASpro supports building complex design matrices, by which complex experimental designs that may include replications, treatments, locations and times, can be accounted for in the linear mixed model (LMM). GWASpro is optimized to handle GWAS data that may consist of up to 10 million markers and 10,000 samples from replicable lines or hybrids. GWASpro provides an interface that significantly reduces the learning curve for new GWAS investigators.

 

Address of the bookmark: https://bioinfo.noble.org/GWASPRO/

]]> Rahul Nayak 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/bookmarks/view/41825/hnadock-a-nucleic-acid-docking-server-for-modeling-rnadna%E2%80%93rnadna-3d-complex-structures Thu, 04 Jun 2020 23:19:07 -0500 https://bioinformaticsonline.com/bookmarks/view/41825/hnadock-a-nucleic-acid-docking-server-for-modeling-rnadna%E2%80%93rnadna-3d-complex-structures <![CDATA[HNADOCK: a nucleic acid docking server for modeling RNA/DNA–RNA/DNA 3D complex structures]]> The HNADOCK server is to predict the binding complex structure between two nucleic acid molecules through a hierarchical docking algorihtm of an FFT-based global search strategy and an intrinsic scoring function for nucleic acid interactions. Users are required to provide the three-dimensional (3D) structures of the two molecules to be docked. 

Address of the bookmark: http://huanglab.phys.hust.edu.cn/hnadock/

]]> Poonam Mahapatra https://bioinformaticsonline.com/news/view/10810/uk-executive-accused-in-glaxosmithkline-china-probe Wed, 14 May 2014 04:55:42 -0500 https://bioinformaticsonline.com/news/view/10810/uk-executive-accused-in-glaxosmithkline-china-probe <![CDATA[UK executive accused in GlaxoSmithKline China probe]]> Mark Reilly and two other colleagues are also suspected of bribing government officials in Beijing and Shanghai, they said.

Police have handed the case over to prosecutors, officials said.

GSK said it took the allegations "very seriously" and would co-operate with the authorities over the matter.

Chinese authorities announced in July last year that they were investigating GSK, detaining four Chinese GSK executives.

http://www.bbc.com/news/world-asia-china-27403914

]]> phu https://bioinformaticsonline.com/bookmarks/view/37529/bokeh-an-interactive-visualization-library-that-targets-modern-web-browsers-for-presentation Fri, 10 Aug 2018 18:43:08 -0500 https://bioinformaticsonline.com/bookmarks/view/37529/bokeh-an-interactive-visualization-library-that-targets-modern-web-browsers-for-presentation <![CDATA[Bokeh: An interactive visualization library that targets modern web browsers for presentation]]> Bokeh is an interactive visualization library that targets modern web browsers for presentation. Its goal is to provide elegant, concise construction of versatile graphics, and to extend this capability with high-performance interactivity over very large or streaming datasets. Bokeh can help anyone who would like to quickly and easily create interactive plots, dashboards, and data applications.

To get started using Bokeh to make your visualizations, see the User Guide.

To see examples of how you might use Bokeh with your own data, check out the Gallery.

A complete API reference of Bokeh is at Reference Guide.

If you are interested in contributing to Bokeh, or extending the library, see the Developer Guide.

Address of the bookmark: https://bokeh.pydata.org/en/latest/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/39114/plumberan-r-package-that-converts-your-existing-r-code-to-a-web-api Wed, 13 Mar 2019 19:20:10 -0500 https://bioinformaticsonline.com/bookmarks/view/39114/plumberan-r-package-that-converts-your-existing-r-code-to-a-web-api <![CDATA[plumber:An R package that converts your existing R code to a web API]]> plumber allows you to create a REST API by merely decorating your existing R source code with special comments. Take a look at an example.

# plumber.R

#* Echo back the input
#* @param msg The message to echo
#* @get /echo
function(msg=""){
  list(msg = paste0("The message is: '", msg, "'"))
}

#* Plot a histogram
#* @png
#* @get /plot
function(){
  rand <- rnorm(100)
  hist(rand)
}

#* Return the sum of two numbers
#* @param a The first number to add
#* @param b The second number to add
#* @post /sum
function(a, b){
  as.numeric(a) + as.numeric(b)
}

Address of the bookmark: https://www.rplumber.io/

]]> BioJoker https://bioinformaticsonline.com/news/view/42370/ncbi-blast-have-added-new-columns-to-the-descriptions Tue, 01 Dec 2020 09:56:07 -0600 https://bioinformaticsonline.com/news/view/42370/ncbi-blast-have-added-new-columns-to-the-descriptions <![CDATA[NCBI BLAST have added new columns to the Descriptions]]> NCBI BLAST have added new columns to the Descriptions Table for web BLAST output. The new columns are  Scientific Name, Common Name, Taxid, and Accession Length. Common Name and Accession Length are now part of the default display. You can click 'Select columns' or 'Manage columns' to add or remove columns from the display Your preferences will be saved for your next visit to BLAST, and when you download your results, whatever columns you have displayed will be saved. See the NCBI Insights post (https://go.usa.gov/x7fPE) for more details.

]]> Neel