<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/27094?offset=180 https://bioinformaticsonline.com/bookmarks/view/29992/spines Mon, 28 Nov 2016 05:33:26 -0600 https://bioinformaticsonline.com/bookmarks/view/29992/spines <![CDATA[Spines]]> Spines is a collection of software tools, developed and used by the Vertebrate Genome Biology Group at the Broad Institute. It provides basic data structures for efficient data manipulation (mostly genomic sequences, alignments, variation etc.), as well as specialized tool sets for various analyses. It also features three sequence alignment packages: Satsuma, a highly parallelized program for high-sensitivity, genome-wide synteny; Papaya, an all-purpose alignment tool for less diverged sequences; and SLAP, a context-sensitive local aligner for diverged sequences with large gaps.

Access Spines here.

Address of the bookmark: https://www.broadinstitute.org/genome-sequencing-and-analysis/spines

]]> Jit https://bioinformaticsonline.com/bookmarks/view/30701/harvest Tue, 31 Jan 2017 10:57:56 -0600 https://bioinformaticsonline.com/bookmarks/view/30701/harvest <![CDATA[Harvest]]> Harvest is a suite of core-genome alignment and visualization tools for quickly analyzing thousands of intraspecific microbial genomes, including variant calls, recombination detection, and phylogenetic trees.

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Tools

  • Parsnp - Core-genome alignment and analysis
  • Gingr - Interactive visualization of alignments, trees and variants
  • HarvestTools - Archiving and postprocessing

Citation

Treangen TJ, Ondov BD, Koren S, Phillippy AM. The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes. Genome Biology, 15 (11), 1-15 [PDF]

Address of the bookmark: http://harvest.readthedocs.io/en/latest/index.html

]]> Jit https://bioinformaticsonline.com/bookmarks/view/32376/diamond Thu, 27 Apr 2017 04:21:54 -0500 https://bioinformaticsonline.com/bookmarks/view/32376/diamond <![CDATA[DIAMOND]]> DIAMOND is a sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000.

More at file:///home/urbe/Downloads/diamond_manual.pdf

http://www.nature.com/nmeth/journal/v12/n1/full/nmeth.3176.html

Address of the bookmark: https://github.com/bbuchfink/diamond

]]> Jit https://bioinformaticsonline.com/bookmarks/view/30698/itol-interactive-tree-of-life Tue, 31 Jan 2017 05:56:30 -0600 https://bioinformaticsonline.com/bookmarks/view/30698/itol-interactive-tree-of-life <![CDATA[iTOL: interactive Tree Of Life]]> Interactive Tree Of Life is an online tool for the display and manipulation of phylogenetic trees. It provides most of the features available in other tree viewers, and offers a novel circular tree layout, which makes it easy to visualize mid-sized tree (up to several thousand leaves). Trees can be exported to several graphical formats, both bitmap and vector based.

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There are several pre-computed trees available for display, including the main Tree Of Life, described in Ciccarelli, et al., 2006. In addition to the precomputed trees, users can upload and display personal trees and data, using the 'Data upload' page or through a personal user account.

Address of the bookmark: http://itol.embl.de/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/37584/mulan-multiple-sequence-local-alignment-and-visualization-for-studying-function-and-evolution Fri, 24 Aug 2018 09:50:01 -0500 https://bioinformaticsonline.com/bookmarks/view/37584/mulan-multiple-sequence-local-alignment-and-visualization-for-studying-function-and-evolution <![CDATA[Mulan: Multiple-sequence local alignment and visualization for studying function and evolution]]> Mulan: Multiple-sequence local alignment and visualization for studying function and evolution

Mulan (http://mulan.dcode.org/), a novel method and a network server for comparing multiple draft and finished-quality sequences to identify functional elements conserved over evolutionary time. Mulan brings together several novel algorithms: the TBA multi-aligner program for rapid identification of local sequence conservation, and the multiTF program for detecting evolutionarily conserved transcription factor binding sites in multiple alignments. In addition, Mulan supports two-way communication with the GALA database; alignments of multiple species dynamically generated in GALA can be viewed in Mulan, and conserved transcription factor binding sites identified with Mulan/multiTF can be integrated and overlaid with extensive genome annotation data using GALA.

Address of the bookmark: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC540288/

]]> Jit https://bioinformaticsonline.com/opportunity/view/843/structural-polymorphism-analysis-from-ngs-data Sat, 13 Jul 2013 17:12:47 -0500 <![CDATA[Structural polymorphism analysis from NGS data]]> The LabEx BASC (Biodiversity, Agroecosystems, Society, Climate), a network of 13 laboratories of the Paris-Saclay Scientific Cluster, is seeking a bioinformatician to analyze Next Generation Sequencing (NGS) data analysis. In the context of a flagship project aiming at understanding and improving the adaptive capacity of agroecosystems it will be critical to establish a link between sequence variation, functional variation, gene/protein expression and phenotypic adaptation.

The successful candidate will be in charge of the detection of polymorphisms including structural variants, of the comparison of multiple and diverse genomes of a same species and of the construction of pan- and core-genomes. These challenging tasks will require bioinformatics developments and implementation of methods for accommodating the high level of repetitiveness of complex genomes. The tools will be integrated into pipelines and made available to end-users through the Galaxy platform. The bioinformatician will therefore also have to provide researchers with advices on their experimental designs in order to ensure compliance of produced datasets with pipelines requirements. He/she will be hosted by a bioinformatics/informatics team (7 people) (http://moulon.inra.fr/index.php/fr/equipestransversales/atelier-de-bioinformatique) which has computational facilities and expertise in NGS data analysis, and will benefit as well from national and international collaborative networks (Aplibio http://www.renabi.fr/platforms/aplibio/, Transplant http://transplantdb.eu, AMAIZING http://www.amaizing.fr/).

The position requires a doctoral degree (PhD) in bioinformatics with strong expertise in script writing (Python/Perl) and pipeline development.

Applicants should send a CV and the names of 2 referees willing to provide a letter of recommendation to joets@moulon.inra.fr.

]]> https://bioinformaticsonline.com/bookmarks/view/32481/sspace Fri, 05 May 2017 05:42:15 -0500 https://bioinformaticsonline.com/bookmarks/view/32481/sspace <![CDATA[SSPACE]]> SSPACE standard is a stand-alone program for scaffolding pre-assembled contigs using NGS paired-read data. It is unique in offering the possibility to manually control the scaffolding process. By using the distance information of paired-end and/or matepair data, SSPACE is able to assess the order, distance and orientation of your contigs and combine them into scaffolds. Currently we offer this as a command-line tool in Perl. The input data is given by pre-assembled contig sequences (FASTA) and NGS paired-read data (Illumina/454/Solid FASTA or FASTQ). The final scaffolds are provided in FASTA format.

 

Address of the bookmark: https://www.baseclear.com/genomics/bioinformatics/basetools/SSPACE

]]> Jit https://bioinformaticsonline.com/pages/view/40248/industrial-training-in-computer-aided-drug-designing-cadd Wed, 13 Nov 2019 05:00:44 -0600 https://bioinformaticsonline.com/pages/view/40248/industrial-training-in-computer-aided-drug-designing-cadd <![CDATA[Industrial Training in Computer Aided Drug Designing (CADD)]]> Learn More about  Computer Aided Drug Designing (CADD)!!!

#rasalsi #rasa In our Industrial program you will get Knowledge on RNA Seq, CHIP Seq,

Batch Starts From 18th November 2019

#hurryup #registernow #enquirenow The primary goal of the industrial training program is to provide students with necessary skills making with employable. RASA LSI trains students with the enhanced skills required for them to excel in jobs in biotechnology, pharmaceuticals, BioIT and related industry sectors. At Rasa you will  learn from industry leaders how to apply these skills in life science & have a command over software developing process  by using various methodologies. For Registration visit us on: https://www.rasalsi.com/index.php/front-page/industrial-training/

]]> RASA Life Sciences https://bioinformaticsonline.com/opportunity/view/2336/3rd-annual-next-generation-sequencing-asia-congress-2013-at-singapore-singapore Wed, 14 Aug 2013 09:55:04 -0500 <![CDATA[3rd Annual Next Generation Sequencing Asia Congress 2013 at Singapore, Singapore]]> The 3rd Annual Next Generation Sequencing Asia Congress is to be held on the 22nd and 23rd of October 2013 in Singapore. Over the 2 days, the conference will provide an overview of the current options of next-generation sequencing platforms, technologies, applications and the newest computational tools for the analysis of next-generation sequencing data and analytical genomics as well as overcoming data management problems. The event will attract over 200 senior-level decision makers working in areas such as next generation sequencing, analytical genomics, computational biology, oncology, RNA profiling, molecular genomics, biomarkers, bioinformatics & data management and clinical & diagnostics development.

Dated : 22 Nov 2013 -23 Nov 2013

http://www.ngsasia-congress.com/

]]> https://bioinformaticsonline.com/opportunity/view/41041/post-doc-computational-biology-bioinformatics-network-biology-data-science-ngs-mfd Sat, 15 Feb 2020 06:13:35 -0600 <![CDATA[Post Doc Computational Biology, Bioinformatics - Network Biology & Data Science, NGS (m/f/d)]]> https://www.jobvector.de/jobs-stellenangebote/biologie-life-sciences/forschung-entwicklung/post-doc-computational-biology-bioinformatics-network-biology-data-science-ngs-129867.html?suid=e522e9793b41817e52ac58d6963b94e2519920df

Requirements
Doctoral degree in Bioinformatics, Computational Biology, (Bio)physics/-mathematics, Biochemistry/Biology or similar with strong quantitative and numeric focus
Ability to numerically process complex and large data sets
Good programming skills (R/Bioconductor and/or Python preferred, Linux is a plus)
Experience in analyzing next-generation sequencing data sets using network biology
Scientific publication record in applied bioinformatics
Familiarity with single cell NGS analyses and other –omics techniques is a plus, but not essential

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