<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/26543?offset=870 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/34940/jpred4-a-protein-secondary-structure-prediction-server Fri, 29 Dec 2017 16:14:28 -0600 https://bioinformaticsonline.com/bookmarks/view/34940/jpred4-a-protein-secondary-structure-prediction-server <![CDATA[JPred4: A Protein Secondary Structure Prediction Server]]> JPred4 (http://www.compbio.dundee.ac.uk/jpred4) is the latest version of the popular JPred protein secondary structure prediction server which provides predictions by the JNet algorithm, one of the most accurate methods for secondary structure prediction.

Address of the bookmark: http://www.compbio.dundee.ac.uk/jpred4/

]]> Poonam Mahapatra https://bioinformaticsonline.com/bookmarks/view/36849/glean-an-unsupervised-learning-system-to-integrate-disparate-sources-of-gene-structure-evidence Sat, 02 Jun 2018 07:38:33 -0500 https://bioinformaticsonline.com/bookmarks/view/36849/glean-an-unsupervised-learning-system-to-integrate-disparate-sources-of-gene-structure-evidence <![CDATA[GLEAN: an unsupervised learning system to integrate disparate sources of gene structure evidence]]> GLEAN is an unsupervised learning system to integrate disparate sources of gene structure evidence (gene model predictions, EST/protein genomic sequence alignments, SAGE/peptide tags, etc) to produce a consensus gene prediction, without prior training.

Address of the bookmark: https://sourceforge.net/projects/glean-gene/

]]> Poonam Mahapatra https://bioinformaticsonline.com/bookmarks/view/42405/caretta-%E2%80%93-a-multiple-protein-structure-alignment-and-feature-extraction-suite Fri, 18 Dec 2020 02:09:44 -0600 https://bioinformaticsonline.com/bookmarks/view/42405/caretta-%E2%80%93-a-multiple-protein-structure-alignment-and-feature-extraction-suite <![CDATA[Caretta – A multiple protein structure alignment and feature extraction suite]]> Caretta – a multiple protein structure alignment and feature extraction suite

Caretta, a multiple structure alignment suite meant for homologous but sequentially divergent protein families which consistently returns accurate alignments with a higher coverage than current state-of-the-art tools. Caretta is available as a GUI and command-line application and additionally outputs an aligned structure feature matrix for a given set of input structures, which can readily be used in downstream steps for supervised or unsupervised machine learning. 

Address of the bookmark: http://www.bioinformatics.nl/caretta/

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/9695/learn-genetics-online Wed, 09 Apr 2014 19:12:42 -0500 https://bioinformaticsonline.com/bookmarks/view/9695/learn-genetics-online <![CDATA[Learn Genetics Online]]> Great source to learn genetics and other relevant stuffs online.

Address of the bookmark: http://learn.genetics.utah.edu/

]]> Rahul Agarwal https://bioinformaticsonline.com/bookmarks/view/44499/severus-a-somatic-structural-variation-sv-caller-for-long-reads Sun, 31 Mar 2024 02:41:27 -0500 https://bioinformaticsonline.com/bookmarks/view/44499/severus-a-somatic-structural-variation-sv-caller-for-long-reads <![CDATA[Severus: a somatic structural variation (SV) caller for long reads]]> Severus is a somatic structural variation (SV) caller for long reads (both PacBio and ONT). It is designed for matching tumor/normal analysis, supports multiple tumor samples, and produces accurate and complete somatic and germline calls. Severus takes advantage of long-read phasing and uses the breakpoint graph framework to model complex chromosomal rearrangements.

If you use Severus, please cite https://www.medrxiv.org/content/10.1101/2024.03.22.24304756v1

Address of the bookmark: https://github.com/KolmogorovLab/Severus

]]> LEGE https://bioinformaticsonline.com/opportunity/view/12111/internship-program-with-arraygen-technolgies Sun, 22 Jun 2014 23:18:31 -0500 <![CDATA[Internship program with ArrayGen Technolgies]]> Internship Program for Bioinformatics / Biotechnology Professionals Currently we offer positions to outstanding students interested in Next Generation Sequencing (NGS) data analysis. Applications are accepted throughout the year. Accepted students will be listed on web with their schedules. Accepted students can attend our future workshops and trainings freely at the specified venue.

Interested candidates may email their resume along with a cover letter to careers@arraygen.com

Official website: http://www.arraygen.com/

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