<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/39372?offset=40 https://bioinformaticsonline.com/fun/view/4196/chemical-elements-of-bioinformatics Tue, 03 Sep 2013 16:35:39 -0500 https://bioinformaticsonline.com/fun/view/4196/chemical-elements-of-bioinformatics <![CDATA[Chemical Elements of Bioinformatics]]> You must be familiar with periodic table and colour pattern, but this time you are going to amaze by new elements table by Eagle genomics. Just check it out and have fun :)

http://elements.eaglegenomics.com/

]]> Rahul Agarwal https://bioinformaticsonline.com/pages/view/36711/ancestral-sequence-reconstruction-steps Fri, 18 May 2018 08:28:26 -0500 https://bioinformaticsonline.com/pages/view/36711/ancestral-sequence-reconstruction-steps <![CDATA[Ancestral sequence reconstruction steps !]]> Ancestral sequence reconstruction (ASR) – also known as ancestral gene/sequence reconstruction/resurrection – is a technique used in the study of molecular evolution. The method consists of the synthesis of an ancestral gene and expression of the corresponding ancestral protein. The idea of protein 'resurrection' was suggested in 1963 by Pauling and Zuckerkandl. Some early efforts were made in the eighties-nineties, led by the laboratory of Steven A. Benner, showing the potential of this technique – one that only started to be fulfilled in the post-genomic era. Thanks to the improvement of algorithms and of better sequencing and synthesis techniques, the method was developed further in the early 2000s to allow the resurrection of a greater variety of and much more ancient genes. Over the last decade, ancestral protein resurrection has developed as a strategy to reveal the mechanisms and dynamics of protein evolution. 
 
BEAST is the best way to predict the ancestral structure. but, I suggest following steps?
 
mafft --maxiterate 1000 --reorder --thread 24 --genafpair Dataset.fasta > Dataset_Alig.fasta
 
2- Your dataset has a good phylogenetic signal, is possible to perform with Tree-Puzzle "http://www.tree-puzzle.de";
 
3 - This dataset which the saturation index, I perform with "http://dambe.bio.uottawa.ca/dambe.asp";
 
4- Has evidence of possible recombination in your dataset, the evaluate if this presence or absence, because this may to influence the grouping of clades, I perform with
---recombination
 
4.1- Phi-test, implemented in SplitTree4"http://www.splitstree.org", (.nex file)
 
4.2- GARD deployed in webserver in the DataMonkey "http://www.datamonkey.org/" - turning to the amino acid seaview -> view proteins -> save as ...) Ideally do a tree-based groups.
 
4.3- RDP4 for download and installation on Windows in "http://web.cbio.uct.ac.za/~darren/rdp.html"
 
4.4- Hyphy (Mac, Windows, Linux) in "http://hyphy.org/w/index.php/Download"
 
4.5- Path-o-Gen (temporal structure of a tree input file -> arquivo.tre)
These steps above, I call of pre-processing to inferences phylogenetic...
 
5- Perform phylogenetic tree, used Bayesian Inference with Molecular Clock, but is necessary Clock Testing:
 
- This step is performed with program Beast (Beauti, Beast and TreeAnnotator), and Tracer_v1.5 more FigTree to inspection.
 
]]> Surabhi Chaudhary https://bioinformaticsonline.com/bookmarks/view/37962/wtdbg2-a-de-novo-sequence-assembler-for-long-noisy-reads-produced-by-pacbio-or-oxford-nanopore Fri, 19 Oct 2018 08:48:43 -0500 https://bioinformaticsonline.com/bookmarks/view/37962/wtdbg2-a-de-novo-sequence-assembler-for-long-noisy-reads-produced-by-pacbio-or-oxford-nanopore <![CDATA[Wtdbg2: a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore]]> Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCONwhile producing contigs of comparable base accuracy.

Address of the bookmark: https://github.com/ruanjue/wtdbg2

]]> Neel https://bioinformaticsonline.com/bookmarks/view/39689/msaprobs-parallel-and-accurate-multiple-sequence-alignment Tue, 09 Jul 2019 23:58:44 -0500 https://bioinformaticsonline.com/bookmarks/view/39689/msaprobs-parallel-and-accurate-multiple-sequence-alignment <![CDATA[MSAProbs - Parallel and accurate multiple sequence alignment]]> MSAProbs is a well-established state-of-the-art multiple sequence alignment algorithm for protein sequences. The design of MSAProbs is based on a combination of pair hidden Markov models and partition functions to calculate posterior probabilities. Assessed using the popular benchmarks: BAliBASE, PREFAB, SABmark and OXBENCH, MSAProbs achieves statistically significant accuracy improvements over the existing top performing aligners, including ClustalW, MAFFT, MUSCLE, ProbCons and Probalign. In addition, MSAProbs is optimized for shared-memory CPUs by employing a multi-threaded design, and further parallelized for distributed-memory systems using MPI to overcome high memory overhead barrier and achieve good parallel and data-size scalability.

Address of the bookmark: http://msaprobs.sourceforge.net/homepage.htm#latest

]]> Neel https://bioinformaticsonline.com/bookmarks/view/40212/kalign-fast-multiple-sequence-alignment-program-for-biological-sequences Fri, 01 Nov 2019 00:20:41 -0500 https://bioinformaticsonline.com/bookmarks/view/40212/kalign-fast-multiple-sequence-alignment-program-for-biological-sequences <![CDATA[Kalign: fast multiple sequence alignment program for biological sequences.]]> Kalign is a fast multiple sequence alignment program for biological sequences.

Align sequences and output the alignment in MSF format:

kalign -i BB11001.tfa -f msf  -o out.msf

Align sequences and output the alignment in clustal format:

kalign -i BB11001.tfa -f clu -o out.clu

Re-align sequences in an existing alignment:

kalign -i BB11001.msf  -o out.afa

Reformat existing alignment:

kalign -i BB11001.msf -r afa -o out.afa

Address of the bookmark: https://github.com/TimoLassmann/kalign

]]> BioStar https://bioinformaticsonline.com/news/view/40789/complete-genome-sequence-of-wuhan-seafood-market-pneumonia-virus-is-out Fri, 31 Jan 2020 02:36:59 -0600 https://bioinformaticsonline.com/news/view/40789/complete-genome-sequence-of-wuhan-seafood-market-pneumonia-virus-is-out <![CDATA[Complete genome sequence of Wuhan seafood market pneumonia virus is out !]]> Wuhan-Hu-1 claimed at least 40 lives and infected at least 1300 others in China. Cases are now being reported from Thailand, Singapore, Malaysia, South Korea, Japan, Vietnam, Nepal, France, Australia and even as far as the US. On Jan 10 2020, while news of the first fatality was barely trickling in, the 29,903 letters constituting the viral genome from an affected individual in Wuhan had already been elucidated (even though a few corrections were made subsequently). All the viral genome sequences from affected individuals are very very close to each other. Several are identical and none has more than 5 differences (99.983% similarity). This strongly suggests that transmission into humans came from a single pointed source and happened very recently, between Sep-Dec 2019.

Check out the detail at https://www.ncbi.nlm.nih.gov/nuccore/MN908947

]]> Jit https://bioinformaticsonline.com/news/view/41300/china%E2%80%99s-bgi-says-it-can-sequence-a-genome-for-just-100 Sat, 29 Feb 2020 04:49:43 -0600 https://bioinformaticsonline.com/news/view/41300/china%E2%80%99s-bgi-says-it-can-sequence-a-genome-for-just-100 <![CDATA[China’s BGI says it can sequence a genome for just $100]]> Using technology originally acquired in the US, the Chinese gene giant BGI Group says it will make genome sequencing cheaper than ever, breaking the $100 barrier for the first time.

The Shenzhen company says the low cost will be possible with an “extreme” DNA sequencing system it plans to offer that is capable of decoding the genomes of 100,000 people a year.

Ref: https://www.technologyreview.com/s/615289/china-bgi-100-dollar-genome/

]]> Neel https://bioinformaticsonline.com/bookmarks/view/43439/mmseqs2-ultra-fast-and-sensitive-sequence-search-and-clustering-suite Wed, 06 Oct 2021 07:01:14 -0500 https://bioinformaticsonline.com/bookmarks/view/43439/mmseqs2-ultra-fast-and-sensitive-sequence-search-and-clustering-suite <![CDATA[MMseqs2: ultra fast and sensitive sequence search and clustering suite]]> MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets. MMseqs2 is open source GPL-licensed software implemented in C++ for Linux, MacOS, and (as beta version, via cygwin) Windows. The software is designed to run on multiple cores and servers and exhibits very good scalability. MMseqs2 can run 10000 times faster than BLAST. At 100 times its speed it achieves almost the same sensitivity. It can perform profile searches with the same sensitivity as PSI-BLAST at over 400 times its speed.

Address of the bookmark: https://github.com/soedinglab/MMseqs2

]]> Abhi 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/42357/irscope-an-online-program-to-visualize-the-junction-sites-of-chloroplast-genomes Wed, 25 Nov 2020 19:44:46 -0600 https://bioinformaticsonline.com/bookmarks/view/42357/irscope-an-online-program-to-visualize-the-junction-sites-of-chloroplast-genomes <![CDATA[IRscope: an online program to visualize the junction sites of chloroplast genomes]]> eMPRess, a software program for phylogenetic tree reconciliation under the duplication-transfer-loss model that systematically addresses the problems of choosing event costs and selecting representative solutions, enabling users to make more robust inferences.

Address of the bookmark: https://sites.google.com/g.hmc.edu/empress/home

]]> Neel