archive-com.com » COM » B » BASECLEAR.COM

Total: 176

Choose link from "Titles, links and description words view":

Or switch to "Titles and links view".
  • Baseclear
    Clinical Diagnostics laboratories Agro Sciences Academic Research institutes About BaseClear Our company Meet our team History Partners Distributors Why BaseClear Reasons to work with BaseClear Research development Quality assurance Technologies Information News Ordering Career Jobs Internships Contact Contact details Contact form Request quotation Order forms Blog Home Our services Lab Products Industries About BaseClear Blog Our company Why BaseClear Information News Ordering Career Jobs Internships Contact Back to overview Release of the BaseClear Genome Browser BGB Our bioinformaticians have now released the BaseClear Genome Browser BGB an easy online platform for high throughput screening of bacterial and fungal genomes Since the introduction of Next Generation Sequencing NGS a massive number of genomes have been sequenced In particular for many bacterial and fungal strains draft assemblies are available which enable researches to perform large scale genomic comparison studies Although considerable effort has been put in to the development of bioinformatics tools such as de novo assembly and annotation it is still challenging to compare multiple genomes and screen these for crucial genomic elements in a simple and intuitive manner With the BGB we introduce an online platform where researchers with or without any bioinformatics training can easily analyse hundreds of annotated genomes using intuitive interfaces and efficient analyses The BGB offers an easy way to screen your annotated genomes either at a project or a taxonomy level The platform allows multiple logins using only a single account and is built on secure connections and encrypted passwords to ensure data integrity BaseClear s platform is available at https annotation baseclear com For information about this platform click here for pricing license fees contact info baseclear com Back to overview More News BaseClear contributes to knowledge of biodiversity and water assessment BaseClear contributes to knowledge of biodiversity and water assessment together with Naturalis

    Original URL path: http://www.baseclear.com/news/Release-of-the-BaseClear-Genome-Browser-%28BGB%29_90_20.html (2016-02-12)
    Open archived version from archive


  • Baseclear
    Contact Contact details Contact form Request quotation Order forms Blog Home Our services Lab Products Industries About BaseClear Blog Our company Why BaseClear Information News Ordering Career Jobs Internships Contact Back to overview Rapid services for fungal genomics From strain to annotated genome in only weeks BaseClear is internationally recognized as an expert in fungal genome sequencing We offer a complete fungal analysis package from DNA isolation to a fully assembled and annotated genome Take advantage of our unique services which is based on a seamless interaction between our NextGen lab and bioinformatics team Super fast and guaranteed delivery time when using our Premium RAPID run service Direct contact with our project managers Optimized service for High throughput projects Excellent bioinformatics services such as de novo assembly and Augustus annotation Easy to interpret output formats Interactive genome mining using our online Genome Browser free year license included Optional advanced genome closure using PacBio SMRT sequencing reads up to 20 kpb FUNGAL RNA SEQUENCING RELIABLE GENE EXPRESSION AND TRANCRIPTOME ANALYSIS BaseClear is the best partner when it comes to RNA Seq analysis on fungal transcriptomes Our expertise and professional support ensures your project will be a success BaseClear service does not stop with the delivery of results We aim to ensure that you can easily interpret the results and use them to make the right decisions HIGH THROUGHPUT GENOME SEQUENCING BaseClear has recently brought genome sequencing and analyses to the next lever by introducing a high throughput genome sequencing facility The option to sequence large numbers of genomes is now viable and the resultant database may deliver considerable value as a screening and discovery tool BaseClear offers a full solution for sequencing existing and novelstrains and analyzing and annotating genome sequences that will be made available as a database which can

    Original URL path: http://www.baseclear.com/news/Rapid-services-for-fungal-genomics-From-strain-to-annotated-genome-in-only-weeks!_90_19.html (2016-02-12)
    Open archived version from archive

  • SSPACE-standard - BaseClear
    Quality assurance Technologies Information News Ordering Career Jobs Internships Contact Contact details Contact form Request quotation Order forms Blog Home Our services Lab Products Industries About BaseClear Blog Next Gen sequencing Bioinformatics Assembly and annotation Comparative genomics RNA seq analysis Microbial profiling analysis Interactive online platforms BaseTools software Sanger sequencing Microbiology Synthetic Biology SSPACE STANDARD 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 SSPACE has shown excellent performance on various datasets The results have been published in the high impact journal Bioinformatics 2011 vol 27 4 pag 578 9 but the method is also frequently cited in other papers Recently SSPACE has been evaluated with a number of competitors in a study conducted by Hunt et al from the Sanger Institute The paper A comprehensive evaluation of assembly scaffolding tools Genome Biology 2014 15 R42 demonstrates SSPACE produces high quality scaffolds and recommend to use our tool Moreover the software is extremely simple to install and run and has a very short running time OBTAINING SSPACE STANDARD In principal the basic version of SSPACE standard is free for academics upgrades are available against a small additional fee Commercial users need in any case to pay for a license the exact fee depends on the size of the

    Original URL path: http://www.baseclear.com/genomics/bioinformatics/basetools/SSPACE (2016-02-12)
    Open archived version from archive

  • Baseclear - GapFiller
    disposables Lab equipment Microparticles Industries Industrial Biotechnology Food Ingredients Pharma Health Water Environment Clinical Diagnostics laboratories Agro Sciences Academic Research institutes About BaseClear Our company Meet our team History Partners Distributors Why BaseClear Reasons to work with BaseClear Research development Quality assurance Technologies Information News Ordering Career Jobs Internships Contact Contact details Contact form Request quotation Order forms Blog Home Our services Lab Products Industries About BaseClear Blog Next Gen sequencing Bioinformatics Assembly and annotation Comparative genomics RNA seq analysis Microbial profiling analysis Interactive online platforms BaseTools software Sanger sequencing Microbiology Synthetic Biology GAPFILLER GapFiller is a stand alone program for closing gaps within pre assembled scaffolds It is unique in offering the possibility to manually control the gap closure process By using the distance information of paired read data GapFiller seeks to close the gap from each edge in an iterative manner From a good number of tests we see the program yields excellent results both on bacterial en eukaryotic data sets The command line Perl script and additional files can be downloaded below The input data is given by pre assembled scaffold sequences FASTA and NGS paired read data FASTA or FASTQ The final gap filled scaffolds are provided in FASTA format GapFiller has been published in Genenome Biology 2012 13 6 56 http genomebiology com content 13 6 R56 In principal the basic version of GapFiller is free for academics upgrades are available against a small additional fee Commercial users need in any case to pay for a license the exact fee depends on the size of the institution number of employees and the type of usage R D or commercial services If you are interested in a copy of our software please fill in your contact details below Note that our software is distributed on a

    Original URL path: http://www.baseclear.com/genomics/bioinformatics/basetools/gapfiller (2016-02-12)
    Open archived version from archive

  • Baseclear
    start a challenging and promising project focusing on the early detection of the development of various diabetic complications in one single mouse model that closely mimics the human situation This two year project aims to deliver a predictive translational model in which the effect of potential new medicines can be evaluated at one early time point in disease development This is a unique approach since normally for every diabetic complication a different animal model is used This new approach will reduce time to market of potential new medicines and strongly reduce the number of animals used in preclinical R D Thereby this project fits into the goal for the replacement reduction and refinement of animal studies The development of new medicines asks a lot of time and effort for the evaluation of their safety PK and efficacy Within the ZonMw funded program More knowledge with less animals TNO has started a collaboration with the Netherlands based academic centers University Medical Center Utrecht and Radboud Proteomics Center the Dutch companies BaseClear B V and Good Biomarker Sciences the US based companies Seventh Wave Laboratories and KineMed Inc and Takeda Pharmaceutical Company Limited in Japan New in the approach of this consortium is that we will combine a large set of state of the art technologies such as ECM protein turnover analysis technology with deuterated water transcriptomics by mRNAseq on a NextGen sequencer proteomics profiling histopathological and biomarker analyses in very small quantities of samples It is this data integration and Systems Biology approach that will help us to find a set of markers signatures that predict the onset of multiple diabetic complications such as non alcoholic steatohepatitis NASH diabetic nephropathy atherosclerosis and retinopathy The availability of such signatures is key in the early evaluation of efficacy and safety of new medicines

    Original URL path: http://www.baseclear.com/news/BaseClear-collaborates-in-TNO-led-consortium-for-a-new-approach-in-early-detection-of-diabetes_90_21.html (2016-02-12)
    Open archived version from archive

  • Baseclear - Full 24H sequencing
    Sanger sequencing Project sequencing Single runs 96 well plates Fragment analysis SNP and VNTR analysis Microbiology Synthetic Biology FULL 24H SEQUENCING Full sequencing means full service and a high quality This option guarantees the best sequencing results when it comes to read length quality of data and customer wishes Sequencing runs are analysed by KB basecaller and reviewed manually Reactions that do not meet our quality standards are repeated if necessary under specific conditions at no additional charge You will receive a full report of the sequencing reaction including sequence data in FASTA SCF and ABI format Results are delivered within 1 working day and before 10 a m Our Full 24H sequencing service in short Optional PCR product purification or plasmid isolation DNA concentration of samples will be measured using fluorescence measurement prior to the sequencing reaction in order to obtain optimal results Single sequencing reaction with a run time corresponding to either 1 100 nt long run or 550 nt short run Sequencing data are automatically analysed by KB caller the international standard software for superior base calling and sequence data interpretation Sequence runs are reviewed manually by our specialists Sequence runs that do not meet our quality criteria are repeated if necessary under specific conditions at no additional charge multiple re runs You will receive a full report of the sequencing reaction including sequence data in FASTA SCF and ABI format Delivery time 1 working day results sent before 10 a m SAMPLE DELIVERY Bacteria for plasmid isolation miniprep on a agar plate or as glycerol stock Purified plasmid in a minimal volume of 30 ul with a DNA concentration of 50 200 ng ul Purified or Raw PCR product in a minimal volume of 30 ul with a DNA concentration 5 ng μl 2 μl of

    Original URL path: http://www.baseclear.com/genomics/sanger-sequencing/full-24h-sequencing (2016-02-12)
    Open archived version from archive

  • Baseclear - Quick Shot
    QUICK SHOT SEQUENCING The Quick Shot service is our flexible and convenient sequencing service at a competitive price for research purposes Samples can be submitted as sample and primer separate or as premixes of purified DNA and primer Data analysis occurs automatically by KB basecaller the international standard software for superior base calling and sequence data interpretation One automatic re run of reactions that do not meet our quality standards is included in this service Delivery time is 1 2 working days after we receive the samples Our Quick Shot sequencing service in short Separate sample and primer or premix possible Free usage of our universal primers see standard primer list Single sequencing reaction with a run time corresponding to either 1 100 nt long run or 550 nt short run Data analysis occurs automatically by KB caller the international standard software for superior base calling and sequence data interpretation You will receive a full report of the sequencing reaction including sequence data in FASTA and SCF and ABI format No manual data editing One automatic re run of reactions that do not meet our quality standards Delivery time 1 2 working days SAMPLE DELIVERY QUICK SHOT SEPARATE SAMPLES Bacteria for plasmid isolation miniprep on a agar plate or as glycerol stock Purified plasmid in a minimal volume of 30 ul with a DNA concentration of 50 200 ng ul Purified or Raw PCR product in a minimal volume of 30 ul with a DNA concentration 5 ng μl 2 μl of the PCR product on agarose gel should give a single clear and sharp band DNA preferably column purified dissolved in water or 10mM Tris pH8 0 Please note that DNA samples should be free of EDTA and ethanol since trace amounts of these compounds will inhibit the sequence

    Original URL path: http://www.baseclear.com/genomics/sanger-sequencing/quick-shot (2016-02-12)
    Open archived version from archive

  • Baseclear - Prepaid BarCode sequencing
    our team History Partners Distributors Why BaseClear Reasons to work with BaseClear Research development Quality assurance Technologies Information News Ordering Career Jobs Internships Contact Contact details Contact form Request quotation Order forms Blog Home Our services Lab Products Industries About BaseClear Blog Next Gen sequencing Bioinformatics Sanger sequencing Project sequencing Single runs 96 well plates Fragment analysis SNP and VNTR analysis Microbiology Synthetic Biology PREPAID BARCODE SEQUENCING Our prepaid BarCode sequencing is the most cost effective option in our sequencing portfolio First the customer orders prepaid BarCode stickers each sticker is valid for one sequencing reaction The customer premixes purified DNA and primer in one of our BaseClear Traxis tubes which can be ordered for free with our BaseBox service Data analysis occurs automatically by KB basecaller the international standard software for superior base calling and sequence data interpretation No rerun of failed reactions is included in this service Delivery time is 1 2 working days after we receive the samples BaseClear s prepaid BarCode sequencing service in short Prepaid BarCode stickers can be ordered through our online order portal Samples must be submitted in one of our BaseClear Traxis tubes which can be ordered for free with our BaseBox service DNA purification and premixing with primer is done by the customer Single sequencing reaction with a long run time corresponding up to 1100 bp Data analysis occurs automatically by KB caller the international standard software for superior base calling and sequence data interpretation You will receive a full report of the sequencing reaction including sequence data in FASTA and SCF and ABI format No manual data editing No rerun of failed reactions Delivery time 1 2 working days after we receive the samples SAMPLE DELIVERY PREMIX of purified DNA and primer For purified plasmid samples submit 0 75 g

    Original URL path: http://www.baseclear.com/genomics/sanger-sequencing/prepaid-barcode-sequencing (2016-02-12)
    Open archived version from archive



  •