<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/26539?offset=890 https://bioinformaticsonline.com/blog/view/44516/16srna-database-download Wed, 24 Apr 2024 04:33:15 -0500 https://bioinformaticsonline.com/blog/view/44516/16srna-database-download <![CDATA[16sRNA Database Download]]> Downloading 16S rRNA databases can be crucial for various bioinformatics analyses, especially in microbiome research. However, it's important to note that databases can vary based on your specific needs, such as the taxonomic coverage you require or the type of analysis you're performing. Here's a general guideline on how you can obtain 16S rRNA databases:

  1. NCBI (National Center for Biotechnology Information):

    • NCBI provides various databases related to genetic information, including 16S rRNA sequences.
    • You can access the 16S ribosomal RNA sequences from NCBI's Nucleotide database (https://www.ncbi.nlm.nih.gov/nucleotide/).
    • Perform a search using keywords like "16S rRNA" or specific bacterial names to find relevant sequences.
    • You can download sequences individually or in batches using the provided tools.

  2. GreenGenes:

    • GreenGenes is a widely used 16S rRNA gene sequence database.
    • You can access it at http://greengenes.secondgenome.com/.
    • GreenGenes provides precompiled databases for various purposes, including classification, alignment, and phylogenetic analysis.

  3. SILVA:

    • SILVA (https://www.arb-silva.de/) is another comprehensive database for ribosomal RNA (rRNA) sequences.
    • It covers not only 16S rRNA but also other ribosomal RNA sequences.
    • SILVA provides precompiled databases for various purposes, including taxonomic classification and alignment.

  4. Ribosomal Database Project (RDP):

    • RDP (http://rdp.cme.msu.edu/) is a curated database that offers 16S rRNA sequences.
    • It provides tools for sequence analysis and classification.
    • You can download sequences and taxonomy information from their website.

  5. QIIME (Quantitative Insights Into Microbial Ecology):

    • QIIME (https://qiime2.org/) is a widely used bioinformatics platform for microbiome analysis.
    • It provides tools for analyzing microbial communities, including processing 16S rRNA sequences.
    • QIIME often includes its own preprocessed 16S rRNA databases that can be used for analysis within the platform.

Before downloading any database, make sure to read the terms of use and citation requirements, as some databases may have specific usage policies. Additionally, consider the compatibility of the database with your analysis pipeline and software tools.

 

NCBI 16s RNA database location ftp://ftp.ncbi.nih.gov/blast/db/16SMicrobial.tar.gz

]]> LEGE https://bioinformaticsonline.com/researchlabs/view/852/queensland-centre-for-medical-genomics-grimmond-lab Sun, 14 Jul 2013 11:58:34 -0500 <![CDATA[Queensland Centre for Medical Genomics, Grimmond Lab]]> Queensland Centre for Medical Genomics

Research Area:
pancreatic cancer; ovarian cancer; prostate cancer; bowel cancer; brain cancer; endometrial cancer; breast cancer; personalised medicine; high-throughput genomics

Link @ http://www.imb.uq.edu.au/sean-grimmond

]]> https://bioinformaticsonline.com/opportunity/view/4725/complex-systems-from-physics-to-biology-october-15-16-2013-at-jnu-convention-center Mon, 23 Sep 2013 10:17:17 -0500 <![CDATA[Complex Systems: From Physics to Biology October 15-16 2013 at JNU Convention Center]]> The symposium intents to focus on complex systems arising in a variety of settings in physics and biology. In particular, applications of the concepts of physics to biological sciences will be the major theme of this meeting.

Selected Topics:

Cluster Dynamics
Non-equilibrium Statistical Mechanics
Forced Systems
Hamiltonian Dynamics
Synchronization & Control
Genomics & Systems Biology
Computational Neuroscience
Econophysics

More @ http://www.jnu.ac.in/Conference/SCS2013/

]]> https://bioinformaticsonline.com/researchlabs/view/863/rolland-lagan-lab Sun, 14 Jul 2013 12:57:57 -0500 <![CDATA[Rolland-Lagan lab]]> The Rolland-Lagan lab at the University of Ottawa is specializing in computational and developmental biology. We use a combination of experimental work, microscopy, image analysis and computer simulations to explore developmental mechanisms in two and three dimensions.

Research Area

Developmental biology, Computational biology, Simulation modeling, Image data analysis

Link @ http://mysite.science.uottawa.ca/arolland/index.html

]]> https://bioinformaticsonline.com/bookmarks/view/34041/r-tuorial Mon, 31 Jul 2017 08:41:40 -0500 https://bioinformaticsonline.com/bookmarks/view/34041/r-tuorial <![CDATA[R tuorial]]> R learning resources

https://flowingdata.com/

Address of the bookmark: https://flowingdata.com/

]]> Rahul Nayak https://bioinformaticsonline.com/blog/view/43008/list-of-useful-machine-ai-learning-resources Tue, 30 Mar 2021 08:56:06 -0500 https://bioinformaticsonline.com/blog/view/43008/list-of-useful-machine-ai-learning-resources <![CDATA[List of useful machine / ai learning resources !]]> ML cheatsheet !

https://github.com/remicnrd/ml_cheatsheet

Visual AI / ML

https://setosa.io/ev/

Simple and efficient tools for predictive data analysis

https://scikit-learn.org/stable/

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/43563/apache-server-setting Fri, 29 Oct 2021 04:29:51 -0500 https://bioinformaticsonline.com/bookmarks/view/43563/apache-server-setting <![CDATA[Apache server setting !]]> Apache is an open source web server that’s available for Linux servers free of charge.

In this tutorial we’ll be going through the steps of setting up an Apache server.

What you’ll learn

  • How to set up Apache
  • Some basic Apache configuration

Address of the bookmark: https://ubuntu.com/tutorials/install-and-configure-apache#3-creating-your-own-website

]]> Abhi https://bioinformaticsonline.com/bookmarks/view/44543/seeing-theory-and-learn Tue, 04 Jun 2024 00:31:54 -0500 https://bioinformaticsonline.com/bookmarks/view/44543/seeing-theory-and-learn <![CDATA[Seeing Theory and Learn]]> Seeing Theory was created by Daniel Kunin while an undergraduate at Brown University. The goal of this website is to make statistics more accessible through interactive visualizations (designed using Mike Bostock’s JavaScript library D3.js).

Address of the bookmark: https://seeing-theory.brown.edu/

]]> LEGE https://bioinformaticsonline.com/bookmarks/view/44620/diy-transcriptomics Wed, 31 Jul 2024 01:19:26 -0500 https://bioinformaticsonline.com/bookmarks/view/44620/diy-transcriptomics <![CDATA[DIY Transcriptomics]]> A semester-long course covering best practices for the analysis of high-throughput sequencing data from gene expression (RNA-seq) studies, with a primary focus on empowering students to be independent in the use of lightweight and open-source software using the R programming language and the Bioconductor suite of packages. This course follows a hybrid format in which online lectures are paired with in-person labs where students participate in hands-on, live coding exercises using real ‘omic datasets. The course is focused on datasets and topics central to infectious disease research, immunology, and One-Health, but the concepts and approaches covered are applicable to any genomic study.

https://diytranscriptomics.com

Address of the bookmark: https://diytranscriptomics.com

]]> Abhi https://bioinformaticsonline.com/bookmarks/view/43273/understanding-kmer Wed, 18 Aug 2021 04:27:51 -0500 https://bioinformaticsonline.com/bookmarks/view/43273/understanding-kmer <![CDATA[Understanding kmer !]]> What is a k-mer anyway? A k-mer is just a sequence of k characters in a string (or nucleotides in a DNA sequence). Now, it is important to remember that to get all k-mers from a sequence you need to get the first k characters, then move just a single character for the start of the next k-mer and so on. Effectively, this will create sequences that overlap in k-1 positions.

Address of the bookmark: https://bioinfologics.github.io/post/2018/09/17/k-mer-counting-part-i-introduction/

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