<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/26925?offset=1380 https://bioinformaticsonline.com/news/view/28199/genome-workbench-2107 Fri, 01 Jul 2016 12:09:59 -0500 https://bioinformaticsonline.com/news/view/28199/genome-workbench-2107 <![CDATA[Genome Workbench 2.10.7]]> Genome Workbench 2.10.7 is here! New features include added support for local custom BLAST databases and improvements to Tree View.

For the full list of features, improvements and fixes, see the release notes:https://ncbi.nlm.nih.gov/tools/gbench/releasenotes

New Features

  • BLAST Tool: added support for local custom BLAST databases
  • Graphical Sequence View: added log scaling option for graph tracks
  • Generic Table View: new tutorial added

Bug Fixes and Improvements

  • Project Tree View: Genomic Collections/Assemblies now show accessions, not just names
  • Tree View: layout updated to better accommodate nodes of different sizes
  • Table Import Dialog (MacOS): fixed issue with table visibility
  • Fixed bug where different molecules IDs in GenBank could resolve to the same sequence
  • Graphical Sequence View: fixed issue where sequence track was not shown for some sequences
  • Graphical Sequence View: fixed protein coloration methods
  • Graphical Sequence View: improved rendering of Markers to better indicate boundaries and produce higher quality PDF images
  • Create Gene Model tool: fixed scenario when gene model tool failed with local sequences
  • Search View: ORF Finder – fixed incorrect protein lengths
  • Fixed bug with not opening project file (.gbp) on a click
  • Fixed issues in GVF import
  • Fixed BLAST Search tool against NCBI databases not working
  • Fixed tblastn (protein BLAST) not working in standalone mode
  • Fixed GTF export failure
]]> Gudiya Pal https://bioinformaticsonline.com/bookmarks/view/28290/bioinformatics-tools-and-software Tue, 05 Jul 2016 10:02:26 -0500 https://bioinformaticsonline.com/bookmarks/view/28290/bioinformatics-tools-and-software <![CDATA[Bioinformatics tools and software]]> USEARCH >
Extreme high-throughput sequence analysis. Orders of magnitude faster than BLAST. MUSCLE >
Multiple sequence alignment. Faster and more accurate than CLUSTALW.

 UPARSE >
OTU clustering for 16S and other marker genes. Highly accurate OTU sequences and improved diversity measures. UCHIME >
Chimeric sequence detection. PILER >
De novo genome repeat finder. PILER-CR >
Detection of CRISPR repeats in bacterial genomes. QSCORE >
Compare two multiple alignments for benchmarking. PALS >
Whole-genome alignment. PREFAB >
Protein Reference Alignment Database. MSA benchmark collection >
Selected multiple alignment benchmarks in a standardized FASTA format.

Address of the bookmark: http://drive5.com/software.html

]]> Jit https://bioinformaticsonline.com/opportunity/view/28425/advertisement-for-junior-research-fellowjrf-at-school-of-computational-and-integrative-sciences-jawaharlal-nehru-university Thu, 14 Jul 2016 07:24:53 -0500 <![CDATA[Advertisement for Junior Research Fellow(JRF) at School of Computational and Integrative Sciences Jawaharlal Nehru University]]> Advertisement for Junior Research Fellow(JRF) - (1)

Applications are invited for a post in DST, India funded Project entitled: "Positive and negative impacts of macromolecular crowding agents during target site location by DNA binding proteins – origin of optimal search at physiological ionic concentration (Reference Number: ECR/2016/000188) ''. The selected candidate will be appointed purely on temporary basis, initially for two years as a JRF that may be extended to one year of SRF based on the performance.

Position: Junior Research Fellow (1)

Qualifications & Experience: Candidate must have a consistently good academic record with at least 60% marks in all throughout and must have qualified NET/GATE.

Desirable: Basic knowledge in the field of biophysics, molecular simulations and computational biology are desirable.

Salary: Consolidated Rs. 25,000 per month.

Tenure: The project duration is for three years and the selected candidate would be appointed after an interview. Appointment will be purely on temporary basis as stipulated by the existing rules of the University.

Interested candidates need to send an application to the address mentioned below mentioning the name of the project and post applied for (on the cover of the envelope).

The applications along with CV should be mailed at the address given below. Name, address, contact number and e. mail address of two referees must be enclosed with the application. The last date for the application is July 31st 2016.

Dr. Arnab Bhattacharjee (Principal Investigator)
Assistant Professor
School of Computational and Integrative Sciences
Jawaharlal Nehru University
New Delhi-110067
E-mail: arnab@jnu.ac.in

Note: 1. Only shortlisted candidates will be communicated to appear in the interview at SCIS, JNU and no other communications in this regard will be entertained.

2. No TA/DA will be paid for appearing in interview.

]]> https://bioinformaticsonline.com/opportunity/view/28547/jrf-bioinformatics-at-iit-delhi Mon, 25 Jul 2016 03:26:20 -0500 <![CDATA[JRF Bioinformatics at IIT, Delhi]]> No. IITD/IRD/RP03017/4254/Advertisement No.: IITD/IRD/093/2016
JRF Bioinformatics job vacancies in Indian Institute of Technology Delhi (IIT Delhi)
Title : Elucidation of Pathologically Relevant miRNAs Responsible for Disease Progression and Resistance to Chemotherapy in Chronic Lymphocytic Leukemia (CLL) (RP03017)
Qualification : Candidates having first class B. Tech. / M.Sc. Degree or equivalent in Bioinformatics or Biotechnology with NET qualification. Desirable: Candidates having computer programming skills (C++, Python, Java, Web designing using Materialize frameworks, database management, offline software GUI development) with knowledge of Linux server environment and / or experience in next generation sequencing (NGS) data analysis, MD simulations will be preferred.
No. of Post : 01
Pay Scale : Rs.25,000/-
How to apply
Walk-in test / interview will be held on 04/08/2016, 03.00 p.m. at Committee Room No. 230, Block-I, Department of Biochemical Engineering & Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi-110016.

More at http://ird.iitd.ac.in/sites/default/files/jobs/project/IITD-IRD-093-2016.pdf

]]> https://bioinformaticsonline.com/bookmarks/view/28566/emboss-apps Wed, 27 Jul 2016 06:00:41 -0500 https://bioinformaticsonline.com/bookmarks/view/28566/emboss-apps <![CDATA[EMBOSS Apps]]> The programs are listed in alphabetical order, Look at the individual applications or go to the GROUPS page to search by category.

EMBASSY applications are described in separate documentation for each package.

Applications in the current release

Address of the bookmark: http://emboss.sourceforge.net/apps/release/6.6/emboss/apps/

]]> Jit https://bioinformaticsonline.com/opportunity/view/28602/srf-and-jrf-bioinformatics-at-tezpur-university-napaam Wed, 03 Aug 2016 03:47:38 -0500 <![CDATA[SRF and JRF Bioinformatics at Tezpur University, Napaam]]> Applications are invited for the following temporary positions unde MHRD sponsored Centre of Excellence
in the Department of Computer Science and Engineering (CSE), Tezpur University

Qualification
and Experience : Senior Research Fellow (SRF) and JRF : First Class in M.E/M.Tech in CSE/IT/ECE with research
experience in relevant fields of research (Candidates having valid GATE/NET Score would be preferred).


Fellowship: Rs. 18,000/- per month (fixed)

Duration : 2 (Two) years and may be extended
depending on status of the project

Age Limit: Candidates should not be more than 32 years of
age in case of SRF and 28 years of age in case of JRF and TA. Upper age limit may be relaxed up to 5
years in the case of candidate belonging to SC/ ST/ OBC/ Women/ Differently abled.

How to Apply:
Interested candidates may send their application on plain paper by post along with his/her educational
qualifications, research experience certificates (for SRF), 02 copies of recent passport/stamp size photographs
and contact phone number to Professor D.K Bhattacharyya, Principal Investigator, Department of Computer
Science & Engineering, Tezpur University, Napaam – 784 028, or mail it to dkb@tezu.ernet.in
(or to smh@tezu.ernet.in) within 15 days of publication of this advertisement.

No TA/DA shall
be paid for attending the interview.

For more details: http://www.tezu.ernet.in/ProjectWalkin/Advt-DoRD-CSE-DKB-20-225-6779-A.pdf

]]> https://bioinformaticsonline.com/bookmarks/view/37645/lsc-improving-pacbio-long-read-accuracy-by-short-read-alignment Thu, 06 Sep 2018 16:27:35 -0500 https://bioinformaticsonline.com/bookmarks/view/37645/lsc-improving-pacbio-long-read-accuracy-by-short-read-alignment <![CDATA[LSC: Improving PacBio Long Read Accuracy by Short Read Alignment]]>
  • Added Command line argument support.
  • Multi-stage execution modes.
  • Support for parallelization. Now execution proceeds in batches of long reads the size of which can be set by --long_read_batch_size N.
  • Better compressed intermediate files.
  • Added utilities folder.
  • Added support for multiple short read files.
  • Removed use of configuration file.

    • Address of the bookmark: https://www.healthcare.uiowa.edu/labs/au/LSC/

    ]]>     Abhimanyu Singh     https://bioinformaticsonline.com/opportunity/view/42490/bioinformatics-scientist-%E2%80%93-icmr-computational-genomics-centre Sat, 26 Dec 2020 10:18:29 -0600 <![CDATA[Bioinformatics Scientist – ICMR Computational Genomics Centre]]> ICMR invites online applications, from Indian Citizens, up to 8th January 2020 till 5:30 PM to fill up the following post to be filled purely on a temporary basis under “ICMR Computational Genomics Centre” under Dr. Harpreet Singh, Head, Division of Biomedical Informatics (BMI), ICMR HQRS, New Delhi 110029.
    The Terms & Conditions for the post are as follows:

    a) Scientist-B – UR (2 posts-Bioinformatics) on consolidated salary of Rs.48,000/- pm + HRA

    b) Scientist C – UR (1 post -Bioinformatics) on consolidated salary of Rs. 51,000 pm+ HRA

    c) Scientist B- UR (2 post-Statistics) on a consolidated salary of Rs.48,000/- pm +HRA

    d) Computer Programmer 1 post UR & 1 post SC on a consolidated salary of Rs. 32,500/- pm

    e) Research Assistant -UR 1 post on a consolidated salary of Rs. 31,000/- pm

    More at https://projectjobs.icmr.org.in/sccbioinformatics/uploads/recruitment/Adv_BMI_24122020.pdf

    ]]>         https://bioinformaticsonline.com/bookmarks/view/34246/unicycler-hybrid-assembly-pipeline-for-bacterial-genomes Fri, 10 Nov 2017 03:58:27 -0600 https://bioinformaticsonline.com/bookmarks/view/34246/unicycler-hybrid-assembly-pipeline-for-bacterial-genomes <![CDATA[Unicycler: Hybrid assembly pipeline for bacterial genomes]]> Unicycler is an assembly pipeline for bacterial genomes. It can assemble Illumina-only read sets where it functions as a SPAdes-optimiser. It can also assembly long-read-only sets (PacBio or Nanopore) where it runs a miniasm+Racon pipeline. For the best possible assemblies, give it both Illumina reads and long reads, and it will conduct a hybrid assembly.

    Address of the bookmark: https://github.com/rrwick/Unicycler

    ]]>     Jit     https://bioinformaticsonline.com/bookmarks/view/28807/organellargenomedraw Tue, 16 Aug 2016 08:13:13 -0500 https://bioinformaticsonline.com/bookmarks/view/28807/organellargenomedraw <![CDATA[OrganellarGenomeDRAW]]> OrganellarGenomeDRAW is dedicated to convert genetic information stored in GenBank entries to graphical maps. The input text file has to be in GenBank flat file format, whereas the output format can be chosen among several formats. The application is especially optimized and adapted for the creation of high-quality, detailed circular maps of organellar genomes like the plastid genome (plastome) or the mitochondrial genome (chondriome). Nevertheless, you can upload any GenBank entry. The workflow is devided into three steps. 

    More at http://ogdraw.mpimp-golm.mpg.de/cgi-bin/ogdraw.pl

    Address of the bookmark: http://ogdraw.mpimp-golm.mpg.de/index.shtml

    ]]>     Jit