<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/19980?offset=1460 https://bioinformaticsonline.com/bookmarks/view/41033/clark-fast-accurate-and-versatile-sequence-classification-system Sat, 15 Feb 2020 01:49:01 -0600 https://bioinformaticsonline.com/bookmarks/view/41033/clark-fast-accurate-and-versatile-sequence-classification-system <![CDATA[CLARK: Fast, accurate and versatile sequence classification system]]> CLARK, a method based on a supervised sequence classification using discriminative k-mers. Considering two distinct specific classification problems (see the article for details), namely (1) the taxonomic classification of metagenomic reads to known bacterial genomes, and (2) the assignment of BAC clones and transcript to chromosome arms/centromeres (in the absence of a finished assembly for the reference genome), CLARK outperforms in classification speed and precision the best state-of-the-art methods.

http://clark.cs.ucr.edu/Spaced/

Address of the bookmark: http://clark.cs.ucr.edu/Spaced/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/41959/rna-bloom-a-fast-and-memory-efficient-de-novo-transcript-sequence-assembler Thu, 09 Jul 2020 03:13:06 -0500 https://bioinformaticsonline.com/bookmarks/view/41959/rna-bloom-a-fast-and-memory-efficient-de-novo-transcript-sequence-assembler <![CDATA[RNA-Bloom: a fast and memory-efficient de novo transcript sequence assembler]]> RNA-Bloom is a fast and memory-efficient de novo transcript sequence assembler. It is designed for the following sequencing data types:

  • single-end/paired-end bulk RNA-seq (strand-specific/agnostic)
  • paired-end single-cell RNA-seq (strand-specific/agnostic)
  • nanopore RNA-seq (PCR cDNA/direct cDNA/direct RNA)

Written by Ka Ming Nip ✉️

Address of the bookmark: https://github.com/bcgsc/RNA-Bloom

]]> LEGE 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/bookmarks/view/44508/a-web-based-tool-for-sequence-alignment-statistics-and-innovative-visualization Thu, 04 Apr 2024 01:44:50 -0500 https://bioinformaticsonline.com/bookmarks/view/44508/a-web-based-tool-for-sequence-alignment-statistics-and-innovative-visualization <![CDATA[A web-based tool for sequence alignment statistics and innovative visualization]]> AlignStatPlot, a new R package and online tool that is well-documented and easy-to usefor MSA and post-MSA analysis. This tool performs both traditional and cutting-edge analy-ses on sequencing data and generates new visualisation methods for MSA results. Whencompared to currently available tools, AlignStatPlot provides a robust ability to handle andvisualise diversity data, while the online version will save time and encourage researchersto focus on explaining their findings. It is a simple tool that can be used in conjunction withpopulation genetics software (PDF) AlignStatPlot: An R package and online tool for robust sequence alignment statistics and innovative visualization of big data.

Address of the bookmark: https://bioinformatics.um6p.ma/AlignStatPlot/

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/33887/gview-a-java-application-for-viewing-and-examining-prokaryotic-genomes-in-a-circular-or-linear-context Fri, 14 Jul 2017 07:47:03 -0500 https://bioinformaticsonline.com/bookmarks/view/33887/gview-a-java-application-for-viewing-and-examining-prokaryotic-genomes-in-a-circular-or-linear-context <![CDATA[GView: A Java application for viewing and examining prokaryotic genomes in a circular or linear context]]> GView is a Java application for viewing and examining prokaryotic genomes in a circular or linear context. It accepts standard sequence file formats and an optional style specification file to generate customizable, publication quality genome maps in bitmap and scalable vector graphics formats. GView features an interactive pan-and-zoom interface, a command-line interface for incorporation in genome analysis pipelines, and a public Application Programming Interface for incorporation in other Java applications.

Availability: GView is a freely available application licensed under the GNU Public License. The application, source code, documentation, file specifications, tutorials and image galleries are available at http://gview.ca

Contact: ac.cg.cpsa-cahp@raalesmod.nav.yrag

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2995121/

Address of the bookmark: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2995121/

]]> Abhimanyu Singh https://bioinformaticsonline.com/opportunity/view/24178/essentials-of-statistics-and-data-analysis-using-r Mon, 31 Aug 2015 01:32:12 -0500 <![CDATA[Essentials of Statistics and Data Analysis using R]]> Clinical Development Services Agency (CDSA) is an extramural unit of Translational Health Science and Technology Institute (THSTI), Department of Biotechnology, Ministry of Science & Technology, Government of India. CDSA has a national mandate of strengthening capacity and capability building in the area of Clinical development and Translational Research.

CDSA is pleased to announce a 4 days hands-on training program on “Essentials of Statistics and Data Analysis using R” at ICGEB, Aruna Asaf Ali Road, New Delhi on December 1 – 4, 2015. This will involve developing and enhancing skills to understand basic principles of statistics for summarizing data and use of appropriate statistical tests as well as providing an understanding of data analysis using R. Didactic lectures with practical sessions will be delivered by experienced faculties from AIIMS and Novartis. Live classroom with power point presentations, case studies, mock exercise, practical sessions on R, group work with time for discussion and Q&A sessions are added advantages of this workshop.

Please contact gayatrivishwakarma.cdsa@thsti.res.in or vineetabaloni.cdsa@thsti.res.in for program and registration details.

Please nominate personage or register yourself on or before November 6, 2015 along with the electronic transfer of registration fee.

]]> https://bioinformaticsonline.com/opportunity/view/24298/staff-scientists-at-national-institute-of-plant-genome-research-new-delhi Fri, 04 Sep 2015 22:06:59 -0500 <![CDATA[Staff Scientists at National Institute of Plant Genome Research, New Delhi]]> National Institute of Plant Genome Research, New Delhi is an Autonomous Research Institution funded by Department of Biotechnology, Ministry of Science & Technology, Govt. of India, to pursue research on various aspects of plant genomics. The Institute is also in the process of establishing a NIPGR Translational Centre at Biotech Science Cluster, NCR, Faridabad. NIPGR invites applications from Indian Citizens for filling up the vacant posts on Direct Recruitment basis, as detailed below. The posts are temporary but likely to continue.

Staff Scientists

Specialization: Applicant should have a Ph.D. with excellent academic credentials along with the track record of scientific productivity evidenced by publications/patents/products in the frontier areas of Plant Biology such as, Computational Biology, Genome Analysis and Molecular Mapping, Molecular Mechanism of Abiotic Stress Responses, Nutritional Genomics, Plant Development and Architecture, Plant Immunity, Molecular Breeding, Transgenics for crop improvement and other emerging areas based on plant genomics.

Remuneration: The length of experience and scientific accomplishments/quality of scientific productivity record will be major factors in deciding the level of appointment as Staff Scientist as well as starting salary in the Pay Bands of Rs 15,600-39,100 (with grade pay of 5400), and Rs 37,400-67,000 (with grade pay of 8,700 and 8,900) plus usual allowances admissible to the Central Government employees. However, NIPGR reserves the right to select candidates in the lower grade against the foregoing posts depending upon the qualifications and experience of the candidate. Reservation of posts shall be as per Govt. of India norms. Five posts (SC-2, ST-1, OBC-2) in the Pay Band of Rs 15,600-39,100 with Grade Pay of Rs 5400, are reserved.

More at http://www.nipgr.res.in/careers/vacancies_latest.php#

Apply online at http://www.nipgr.res.in/nipgr_recu/nipgr_recu.php

Form http://www.nipgr.res.in/files/careers/Application_Performa_2015.doc

]]> https://bioinformaticsonline.com/bookmarks/view/31278/metapred2cs Fri, 03 Mar 2017 05:15:07 -0600 https://bioinformaticsonline.com/bookmarks/view/31278/metapred2cs <![CDATA[MetaPred2CS]]> MetaPred2CS Web server is a meta-predictor based on Support Vector Machine (SVM) that combines 6 individual sequence based protein-protein interaction prediction methods to predict prokaryotic two-component system protein-protein interactions (PPIs). The methods implemented in MetaPred2CS are 2 co-evolutionary methods: in-silico two hybrid (i2h) and mirror tree (MT) methods and 4 genomics context based methods: phylogenetic profiling (PP), gene fusion (GF), gene neighbourhood (GN) and and gene operon methods (GO).

 http://metapred2cs.ibers.aber.ac.uk/

Address of the bookmark: https://github.com/martinjvickers/MetaPred2CS

]]> Manisha Mishra https://bioinformaticsonline.com/opportunity/view/27253/ra-bioinformatics-at-jnu-delhi Tue, 10 May 2016 01:50:38 -0500 <![CDATA[R.A Bioinformatics at JNU, Delhi]]> R.A Jobs opportunity in Jawaharlal Nehru University (JNU) on purely temporary basis

Project Title : "Structural and functional characterization of serine biosynthetic pathway enzymes from Entamoeba histolytica"

No. of Post : 01

Qualification : Ph.D in any computational biology / bioinformatics

Desirable : 1. Experience with docking, simulations and structural biology with proof of publications is preferred. 2. National Eligibility Test cleared [CSIR/UGC] candidate is preferred.

Salary : According to CSIR rules
How to apply

The application on plain paper indicating name, date of birth/age, address, essential/technical/professional qualifications. experience, list of publications should reach The Prof. S. Gourinath, Principal Investigator, [Project Director], School of Life Sciences, Jawaharlal Nehru University, New Delhi-110067, on or before 23rd May 2016.

More at http://www.jnu.ac.in/Career/currentjobs.htm

]]> https://bioinformaticsonline.com/opportunity/view/42955/post-doctoral-position-scientist-mfd-in-bioinformatics Mon, 15 Mar 2021 11:34:23 -0500 <![CDATA[Post-doctoral position / Scientist (m/f/d) in Bioinformatics]]> The Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V. in Dortmund is looking for a Post-doctoral position / Scientist (m/f/d) in Bioinformatics

More at

https://www.isas.de/files/redaktion/jobs/2021/18.60.1_Postdoc_deNBI_06_21_AS.pdf

https://www.isas.de/en/news/062021-post-doctoral-position-scientist-mfd-in-bioinformatics

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