<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/41493?offset=300 https://bioinformaticsonline.com/news/view/42626/spades-team-announce-new-version-spades-v315 Fri, 15 Jan 2021 10:24:27 -0600 https://bioinformaticsonline.com/news/view/42626/spades-team-announce-new-version-spades-v315 <![CDATA[SPADes team announce new version SPADes v3.15]]> New SPAdes 3.15.0.0. announced by the SPADes team This release includes such new features as: 
- CoronaSPAdes pipeline for the assembly of transcriptomic and metatranscriptomic data of full-length coronaviridae genomes; 
- Meta-Viral and RNA-Viral pipelines for metagenomic and metatranscriptomic data defining viral genomes; 
-New trusted contiguous use algorithm; 
-Switched to the memory allocator mimalloc; 
- PlasmidSPAdes and bgcSPAdes are now provided as an input assembly graph; 
- Important improvements and corrections to the metaplasmid pipeline; 
- Multiple performance improvements in procedures for simplification and repeat resolving. 
Please, consider updating.

Check out more at https://cab.spbu.ru/software/spades/

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/39674/simka-and-simkamin-are-comparative-metagenomics-method-dedicated-to-ngs-datasets Sat, 06 Jul 2019 13:56:10 -0500 https://bioinformaticsonline.com/bookmarks/view/39674/simka-and-simkamin-are-comparative-metagenomics-method-dedicated-to-ngs-datasets <![CDATA[Simka and SimkaMin are comparative metagenomics method dedicated to NGS datasets]]> Simka is a de novo comparative metagenomics tool. Simka represents each dataset as a k-mer spectrum and compute several classical ecological distances between them.

Developper: Gaëtan Benoit, PhD, former member of the Genscale team at Inria.

Contact: claire dot lemaitre at inria dot fr

Simka and SimkaMin are comparative metagenomics method dedicated to NGS datasets. https://gatb.inria.fr/software/simka/

Address of the bookmark: https://github.com/GATB/simka

]]> Neel https://bioinformaticsonline.com/blog/view/41455/coronavirus-covid-%E2%80%9019-testing-sites-in-india Mon, 16 Mar 2020 16:13:41 -0500 https://bioinformaticsonline.com/blog/view/41455/coronavirus-covid-%E2%80%9019-testing-sites-in-india <![CDATA[Coronavirus COVID ‐19 Testing Sites In India]]> COVID-19 is a new illness that can affect your lungs and airways. It's caused by a virus called coronavirus.

Stay at home if you have coronavirus symptoms

Stay at home if you have either:

  • a high temperature – you feel hot to touch on your chest or back
  • a new, continuous cough – this means you've started coughing repeatedly

DO NOT TAKE

Ibrufen

https://amp.theguardian.com/world/2020/mar/14/anti-inflammatory-drugs-may-aggravate-coronavirus-infection

How to avoid catching and spreading coronavirus (social distancing)

Everyone should do what they can to stop coronavirus spreading.

It is particularly important for people who:

  • are 70 or over
  • have a long-term condition
  • are pregnant
  • have a weakened immune system

image

Below are the 52 Coronavirus COVID-19 Testing sites/locations in India.

State: Andhra Pradesh       

  1. Sri Venkateswara Institute of Medical Sciences, Tirupati
  2. Andhra Medical College, Visakhapatnam, Andhra Pradesh
  3. GMC, Anantapur, AP

State: Andaman & Nicobar islands

  1. Regional Medical Research Centre, Port Blair, Andaman, and Nicobar

State: Assam

  1. Gauhati Medical College, Guwahati
  2.  Regional Medical Research Center, Dibrugarh

State: Bihar

  1. Rajendra Memorial Research Institute of Medical Sciences, Patna

State: Chandigarh

  1. Post Graduate Institute of Medical Education & Research, Chandigarh

State: Chhattisgarh

  1. All India Institute Medical Sciences, Raipur

Union Territory: Delhi-NCT 

  1. All India Institute Medical Sciences, Delhi
  2. National Centre for Disease Control, Delhi

State: Gujarat

  1. BJ Medical College, Ahmedabad
  2. M.P.Shah Government Medical College, Jamnagar

State: Haryana

  1. Pt. B.D. Sharma Post Graduate Inst. of Med. Sciences, Rohtak, Haryana
  2. BPS Govt Medical College, Sonipat

State: Himachal Pradesh

  1. Indira Gandhi Medical College, Shimla, Himachal Pradesh
  2. Dr.Rajendra Prasad Govt. Med. College, Kangra, Tanda, HP

Union Territory: Jammu and Kashmir

  1. Sher‐e‐ Kashmir Institute of Medical Sciences, Srinagar
  2. Government Medical College, Jammu

State: Jharkhand

  1. MGM Medical College, Jamshedpur

State: Karnataka

  1. Bangalore Medical College & Research Institute, Bangalore
  2. National Institute of Virology Field Unit Bangalore
  3. Mysore Medical College & Research Institute, Mysore
  4. Hassan Inst. of Med. Sciences, Hassan, Karnataka
  5. Shimoga Inst. of Med. Sciences, Shivamogga, Karnataka

State: Kerala

  1. National Institute of Virology Field Unit, Kerala
  2. Govt. Medical College, Thiruvananthapuram, Kerala
  3. Govt. Medical College, Kozhikode, Kerala

State: Madhya Pradesh

  1. All India Institute Medical Sciences, Bhopal
  2. National Institute of Research in Tribal Health (NIRTH), Jabalpur

State: Meghalaya

  1. NEIGRI of Health and Medical Sciences, Shillong, Meghalaya

State: Maharashtra

  1. Indira Gandhi Government Medical College, Nagpur
  2. Kasturba Hospital for Infectious Diseases, Mumbai

State: Manipur

  1. J N Inst. of Med. Sciences Hospital, Imphal‐East, Manipur

State: Odisha

  1. Regional Medical Research Center, Bhubaneswar

Union Territory: Puducherry

  1. Jawaharlal Institute of Postgraduate Medical Education & Research, Puducherry

State: Punjab

  1. Government Medical College, Patiala, Punjab
  2. Government Medical College, Amritsar

State: Rajasthan

  1. Sawai Man Singh, Jaipur
  2. Dr. S.N Medical College, Jodhpur
  3. Jhalawar Medical College, Jhalawar, Rajasthan
  4. SP Med. College, Bikaner, Rajasthan

State: Tamil Nadu

  1. King’s Institute of Preventive Medicine & Research, Chennai
  2. Government Medical College, Theni

State: Tripura

  1. Government Medical College, Agartala

State: Telangana

  1. Gandhi Medical College, Secunderabad

State: Uttar Pradesh

  1. King’s George Medical University, Lucknow
  2. Institute of Medical Sciences, Banaras, Hindu University, Varanasi
  3. Jawaharlal Nehru Medical College, Aligarh

State: Uttarakhand

  1. Government Medical College, Haldwani

State: West Bengal

  1. National Institute of Cholera and Enteric Diseases, Kolkata
  2. IPGMER, Kolkata
]]> Neel https://bioinformaticsonline.com/bookmarks/view/43970/covid-spectrum Sun, 25 Sep 2022 18:57:50 -0500 https://bioinformaticsonline.com/bookmarks/view/43970/covid-spectrum <![CDATA[Covid Spectrum !]]> https://cov-spectrum.org/explore/World/AllSamples/

CoV-Spectrum supports a wide range of search queries. The following sections presents search options of the basic search bar. For information on the advanced search

Address of the bookmark: https://cov-spectrum.org/

]]> Abhi https://bioinformaticsonline.com/pages/view/1897/genetic-test-in-india Sun, 11 Aug 2013 10:54:35 -0500 https://bioinformaticsonline.com/pages/view/1897/genetic-test-in-india <![CDATA[Genetic Test in India]]> 1.Xcode Life Sciences Pvt. Ltd.
6B, Eldorado, 
112, Nungambakkam High Road,
Nungambakkam, Chennai 600034
Tamil Nadu, India 

2.Mapmygenome™
Royal Demeure,HUDA Techno Enclave,
Plot No. 12/2, Sector-1 500 081 
Madhapur,Hyderabad
AP, India

3. DNA Labs India

http://www.dnalabsindia.com/lab.php

 

4.MedGenome Labs Pvt Ltd
(Division of SciGenom Labs Pvt Ltd.)
Plot no: 43A,SDF, 3rd floor
A Block,CSEZ, Kakanad, Cochin
Kerala - 682037 
Phone: 0484 - 2413399
Fax: 0484 - 2413398
Email: info@medgenome.com

5.Narayana Nethralaya

Narayana Hrudayalaya Campus
Narayana Health City
# 258/A, Bommasandra, Hosur Road, 
Bangalore - 560 099 - INDIA.
TEL: +91-80-66660655-0658 
FAX: +91-80-66660650 
Mobile: 9902 821128 (Emergency Only)
e-mail: info@narayananethralaya.com

6.BioAxis DNA Research Centre Private Limited
13-51,Sri Lakshmi Nagar colony,
Besides Big Bazar, Near Kamineni Hospitals
GSI Post BandalGuda (L B Nagar) Hydeabad-500068
Andhra Pradesh (India).
Phone : +91-40-24034503/+91-9246338983

7.Gene Guiide

8th Floor, Embassy Towers, 7 Bungalows Rd, Versova, Andheri West, Mumbai-61 
 09167 117799 
 info@geneguiide.com 

See more at: http://www.geneguiide.com

8.INDIAN BIOSCIENCES
Regd. Office:
G-2 (Ground Floor Rear), Kailash Colony, New Delhi - 110048, India.
Phone: +91 (0)11 29236088, Email: info@inbdna.com.

9.SRL Limited

GP-26, MARUTI INDUSTRIAL ESTATE,

UDYOG VIHAR,SECTOR-18,

GURGAON - 122015

Tel: 0124-3001243 / 0124-3001209

SRL Limited
VASANT VIHAR, 8, PALAM MARG,
NEW DELHI - 110057
Tel: 011 - 4229 5333 

Website: http://www.srlworld.com
National Customer care number:
Call Toll Free : 1800-222-660/1800-102-8282 
E-mail id: customercare@srl.in

10.Tata Memorial Centre,

Advanced Centre for Treatment, Research and Education in Cancer

Kharghar, Navi Mumbai - 410 210, INDIA.

Tel: +91-22-2740 5000

Fax: +91-22-2740 5085

E-mail: mail@actrec.gov.in

 

 

]]> Rahul Agarwal https://bioinformaticsonline.com/news/view/5898/an-entire-genome-written-in-lab Fri, 25 Oct 2013 09:43:03 -0500 https://bioinformaticsonline.com/news/view/5898/an-entire-genome-written-in-lab <![CDATA[An entire genome written in lab]]> This is the first time ever the genetic code has been fundamentally changed. The breakthrough is a huge step forward in synthetic biology and opens up the possibility of turning re-coded bacteria into biofactories, capable of producing potent new forms of protein that could fight disease or generate sustainable materials.

More @ http://news.yale.edu/2013/10/17/researchers-rewrite-entire-genome-and-add-healthy-twist

News Reference: Yale news

image

Image Source: Sciencedaily.

]]> Rahul Nayak https://bioinformaticsonline.com/videolist/watch/10664/dna-replication-process-3d-animation Sat, 10 May 2014 04:41:22 -0500 https://bioinformaticsonline.com/videolist/watch/10664/dna-replication-process-3d-animation <![CDATA[DNA Replication Process [3D Animation]]]> See an organised list of all the animations: http://doctorprodigious.wordpress.com/hd-animations/]]> https://bioinformaticsonline.com/blog/view/33874/dna-testing-companies-around-the-globe Thu, 13 Jul 2017 04:44:03 -0500 https://bioinformaticsonline.com/blog/view/33874/dna-testing-companies-around-the-globe <![CDATA[DNA testing companies around the globe !]]> It was realized in the 1940s that DNA molecules are passed down through the generations of a family. In 1953 Watson and Crick elucidated the chemical structure of this molecule as a twisted ladder (a ‘helix’) made of two strands. DNA occurs in all the cells of our body, it is our blueprint! The strands of DNA contain information in the form of a code, which in turn determines our individual traits and characteristics. This code, the genetic code, is the order of four types of DNA building block. When the two strands of DNA separate, each building block (‘base’) accurately templates a corresponding base on the newly made strand of DNA so that information is not lost but is instead duplicated and preserved.

Testing for similarities between DNA (deoxyribonucleic acid) samples from two people allows family relationships to be established – or disproved – to an extraordinarily high degree of certainty. A common use for a DNA test is to establish if a man is the biological father of a child; this is known as a paternity test. However, there are other uses for the science of DNA testing (also called genotyping), these include forensic analysis of human DNA samples, and tracking relationships amongst domesticated animals.

The order in which the bases occur in DNA is referred to as the DNA sequence. Each person is unique and just as people differ in their fingerprints, they also have a unique and slightly different DNA sequence. Half of a person’s DNA is received from their mother, and half is received from the father. However, while fingerprints have no value for establishing family relationships, the minor variations in DNA sequence are extraordinarily useful for this purpose. All cells of our body contain DNA, skin cells from the lining of the cheek provide a simple and convenient source of material.

DNA is purified from these cells and the minor variations are read out as a type of bar-code by a machine. When the net DNA ‘barcodes’ from family members are lined up next to each other it becomes clear when a child is related to biological parents because half the stripes in the bar-code like signature will line up with those of the mother, and half will line up with those of the father. On the other hand, in the absence of a biological relationship, the DNA signatures from a child and from a potential parent are not found to have 50% in common. It may be appreciated that DNA testing is the most convenient and scientifically accurate method of determining relationships between people.

Following are the list of companies who qssist in DNA testing:

DNA testing companies

]]> Jit https://bioinformaticsonline.com/bookmarks/view/43268/kmer-a-suite-of-tools-for-dna-sequence-analysis Wed, 18 Aug 2021 00:02:54 -0500 https://bioinformaticsonline.com/bookmarks/view/43268/kmer-a-suite-of-tools-for-dna-sequence-analysis <![CDATA[Kmer: a suite of tools for DNA sequence analysis]]> More at https://help.rc.ufl.edu/doc/Kmer

This also includes:

  • A2Amapper: ATAC, Assembly to Assembly Comparision tool:
    • Comparative mapping between two genome assemblies (same species), or between two different genomes (cross species).
  • Sim4db:
    • Spliced alignment of cDNA and genomic sequences, from the same (sim4) or related (sim4cc) species. Optimized for high-throughput batched alignment.
  • LEAFF:
    • LEAFF (ahem, Let's Extract Anything From Fasta) is a utility program for working with multi-fasta files. In addition to providing random access to the base level, it includes several analysis functions.
  • Meryl:
    • An out-of-core k-mer counter. The amount of sequence that can be processed for any size k depends only on the amount of free disk space.

Address of the bookmark: https://help.rc.ufl.edu/doc/Kmer

]]> BioStar https://bioinformaticsonline.com/blog/view/38238/list-of-motif-discovery-tools Tue, 20 Nov 2018 03:54:26 -0600 https://bioinformaticsonline.com/blog/view/38238/list-of-motif-discovery-tools <![CDATA[List of motif discovery tools !]]>
In genetics, a sequence motif is a nucleotide or amino-acid sequence pattern that is widespread and has, or is conjectured to have, a biological significance. For proteins, a sequence motif is distinguished from a structural motif, a motif formed by the three-dimensional arrangement of amino acids which may not be adjacent.
 
Following are the list of tools for motif discovery:
 

Perform secondary structure predictions on protein sequences.

Find binding specificity information about DNA-protein complexes.

Find information about the binding specificity of DNA-binding proteins.

Use this web-based sequence motif visualization system to display sequence motif information in its appropriate three-dimensional (3D) context.

Protein function prediction and annotation in an integrated environment powered by web service.

Use to predict function from de novo protein sequences.

Search for short active protein sequences with demonstrated biological activities.

Search for ungapped segments corresponding to the most highly conserved regions of proteins.

Identify and measure surface accessible pockets as well as interior inaccessible cavities, for proteins and other molecules.

To search for catalytic residue annotation for enzymes in the Protein Data Bank.

Predict protein function using Gene Ontology.

Automatically calculate evolutionary conservation scores of key amino acid residues and map them on protein structures.

Mine the protein structure space.

Predict short linear motifs (3-8 residues) in a set of protein sequences.

A web client for visualizing protein sequence feature information using DAS.

Identify the domain architecture within a protein sequence.

Predict functional sites in eukaryotic proteins.

Use a collection of tools for protein analyses.

Predict potential protein post-translational modifications and find potential single amino acid substitutions in peptides.

Search for information related to the catalytic mechanisms of enzymes.

An integrated feature-based function prediction server for vertebrate proteomes.

Identify the closest matching PRINTS sequence motif fingerprints in a protein sequence.

Search for functional annotation of important sites in proteins with known structures.

Produce 3D conformations of small drug compounds.

A database presenting experiment-based results in human proteomics.

Conduct exhaustive intermediate profile searches of a set of homologous protein sequences.

Design protein mutations in site-directed mutagenesis.

Annotate protein using this integrated annotation resource.

Identify protein family (and DNA) domains, patterns, motifs, protein families, and functional sites.

Interactive forecasting of protein interaction hot spots.

Database containing pairs of structural analogs and their alignments.

Find sequence patterns in DNA and protein sequences.

A web server for knowledge-based modeling of protein-peptide complexes, specifically peptides in complex with major histocompatibility complex (MHC) proteins and kinases.

Find structural segments or motifs for protein structures.

Visualize protein sequence motifs on the 3D protein structures.

Find presence of any known protein motif (Prosite and Pfam) in a protein sequence.

Recognize spatial chemical binding patterns common to a set of protein structures.

Analyze proteins for the presence of N-terminal N-myristoylation site.

Find the presence of N-Glycosylation sites in human proteins.

Find the presence of O-GalNAc (mucin type) glycosylation sites in mammalian proteins.

Analyze eukaryotic proteins for the presence of serine, threonine and tyrosine phosphorylation sites.

Find possible kinase specific phosphorylation sites in eukaryotic proteins.

Predict cleavage sites at basic amino acid locations in neuropeptide precursor sequences.

Find information about patented nucleotide and protein sequences.

Search for information about glycoproteins with O-linked and C-linked glycosylation sites.

Find information about protein sequence annotations.

A server to predict protein active site residues.

Search for structural and functional information on the protein functional sites.

Search 3D protein fragments similar in structure to known active, binding and posttranslational modification sites.

Conduct genome wide functional and structural analysis.

Search for phosphorylation data of any protein of interest.

Search for information on prokaryotic proteins that undergo serine, threonine, or tyrosine phosphorylation.

Determine correct names for proteins.

Web application for predicting protein disorder by using physicochemical features and reduced amino acid set of a position-specific scoring matrix.

Find homologous protein-protein interactions across multiple species.

Search your query sequence against PROSITE pattern database for protein motifs.

Find information about protein-RNA complexes from the Protein Data Bank (PDB).

Identify protein families and domains for a given protein sequence.

A comprehensive database of pattern-recognition receptors and their ligands.

Search for short nucleotide or peptide sequences such as cis-elements in nucleotide sequences or small domains and motifs in protein sequences.

Database specialized in documenting human PPBD-containing proteins and PPBD-mediated interactions.

Predicts potential protease cleavage sites and sites cleaved by chemicals in a given protein sequence.

Predict combined transmembrane topology and signal peptides.

Search for eukaryotic phosphorylation sites.

Search for 3D structure and functional annotation of phosphorylation sites in proteins.

Search the database of in vivo phosphorylation sites of human and mouse proteins

Find information about polyglutamine (polyQ) repeats.

Find the presence of protein motifs and patterns in an amino acid sequence.

Predict signal peptide sequences and their cleavage positions in bacterial and eukaryotic amino acid sequences.

Predict protein functions based on known structures.

Predict the location of potential protein-protein binding sites for unbound proteins.

Identify short linear signatures in protein termini.

Analyze and identify newly obtained protein sequences.

Predict protein binding sites in a protein sequence based on geometrical analysis of protein tertiary substructures.

Search for evolutionarily conserved motif-like patterns in protein sequences.

Web-based server for analyzing and predicting RNA binding sites in proteins.

Search for similarities between proteins by simultaneous matching of multiple motifs.

Predict residues in protein sequences that determine the proteins' functional specificity.

Predict specificity-determining residues in protein families.

Find shared motifs in proteins with a common attribute.

Conduct in silico sumoylation sites prediction.

Search for motifs and patterns within protein sequences.

Search for motifs within proteins that are likely to be phosphorylated by specific protein kinases or bind to domains such as SH2 domains, 14-3-3 domains or PDZ domains.

Find information about populations carrying polymorphisms within protein binding pockets that make them susceptible to serious adverse drug reaction (SADR).

Search the presence of a motif in either amino acid sequence or nucleotide sequence.

Predict the presence of tyrosine sulfation sites in protein sequences

Look at protein structure from a ligand and binding site perspective.

Use a collection of bioinformatics tools at this portal site.

Find information about tandem repeats in proteins that carry fundamental biological functions and are related to a number of human diseases.

Find information about functional residues in alpha-helical and beta-barrel membrane proteins.

Database of domains and motifs with conservative location in transmembrane proteins.

Search for highly conserved and specific protein sequence motifs.

Predict functional sites in protein sequence alignments use different methodologies.

Find de novo protein motifs from chromatin immunoprecipitation data.

Scan query structures for functional sites in both proteins and nucleic acids.

Analyze quantitative structure-activity relationship of related protein families.

Search for ungapped alignments of highly conserved regions among a protein family or superfamily.

An expert system for predicting ligand-binding residues in protein structures.

Automatically identify spatially interacting motifs among distantly related proteins sharing similar folds and possessing common ancestral lineage.

]]> Neel