Difference: SequencingBioLab (1 vs. 19)

Revision 19
02 Oct 2014 - Main.PerryMoerland
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META TOPICPARENT name="SupportBioLab"
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Medical Bioinformatics

 

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Revision 18
25 Mar 2011 - Main.BarberaVanSchaik
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META TOPICPARENT name="SupportBioLab"
Medical Bioinformatics

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Revision 17
21 Mar 2011 - Main.AngelaLuijf
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META TOPICPARENT name="SupportBioLab"
Medical Bioinformatics

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Sequence analysis People
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Sequence analysis People
 
Over the past decade we have gained considerable experience with the analysis of nucleotide sequences. Currently, most of our effort is devoted to the analysis of next generation sequencing data that is produced in the AMC sequencing facility (Roche 454 and ABI Solid). We are involved in a large range of projects that often require the development of dedicated methods for the analysis of the data. Examples of such projects include the determination of T-cell variation, virus discovery (metagenomics), identification of alternative splicing and identification of HIV microRNAs.
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Our web-site includes a restricted area for AMC employees with more detailed information about current sequence analysis projects, available software and infrastructure, tips & tricks, etc. If you want access to this area please contact Barbera van Schaik
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Revision 16
31 Jan 2010 - Main.AntoineVanKampen
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META TOPICPARENT name="SupportBioLab"
Medical Bioinformatics

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Revision 15
12 Jan 2010 - Main.BarberaVanSchaik
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META TOPICPARENT name="SupportBioLab"
Medical Bioinformatics

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  For specific projects that require analysis with significant computer time we make use of Grid computing.
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Our web-site includes a restricted area for AMC employees with more detailed information about current sequence analysis projects, available software and infrastructure, tips & tricks, etc. If you want access to this area please contact Barbera van Schaik
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Our web-site includes a restricted area for AMC employees with more detailed information about current sequence analysis projects, available software and infrastructure, tips & tricks, etc. If you want access to this area please contact Barbera van Schaik
 
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Revision 14
22 Dec 2009 - Main.AntoineVanKampen
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META TOPICPARENT name="SupportBioLab"
Medical Bioinformatics

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Sequence analysis
Over the past decade we have gained considerable experience with the analysis of nucleotide sequences. Currently, most of our effort is devoted to the analysis of next generation sequencing data that is produced in the AMC sequencing facility (Roche 454 and ABI Solid). We are involved in a large range of projects that often require the development of dedicated methods for the analysis of the data. Examples of such projects include the determination of T-cell variation, virus discovery (metagenomics), identification of alternative splicing and identification of HIV microRNAs.
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Sequence analysis People
Over the past decade we have gained considerable experience with the analysis of nucleotide sequences. Currently, most of our effort is devoted to the analysis of next generation sequencing data that is produced in the AMC sequencing facility (Roche 454 and ABI Solid). We are involved in a large range of projects that often require the development of dedicated methods for the analysis of the data. Examples of such projects include the determination of T-cell variation, virus discovery (metagenomics), identification of alternative splicing and identification of HIV microRNAs.
 

We have developed several methods and processing pipelines for the (pre-)processing of the data:
  • Re-grouping of sequences based on one or more MIDs/barcodes, primers or other sequence tags
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Our web-site includes a restricted area for AMC employees with more detailed information about current sequence analysis projects, available software and infrastructure, tips & tricks, etc. If you want access to this area please contact Barbera van Schaik
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For more information contact Antoine van Kampen or Barbera van Schaik
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Revision 13
21 Dec 2009 - Main.AntoineVanKampen
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META TOPICPARENT name="SupportBioLab"
Medical Bioinformatics

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Back to menuSort

Changed:
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Sequence analysis

Over the past decade we have gained considerable experience with the analysis of nucleotide sequences. Currently, most of our effort is devoted to the analysis of next generation sequencing data that is produced in the AMC sequencing facility (Roche 454 and ABI Solid). We are involved in a large range of projects that often require the development of dedicated methods for the analysis of the data. Examples of such projects include the determination of T-cell variation, virus discovery (metagenomics), identification of alternative splicing and identification of HIV microRNAs.
>
>
Sequence analysis
Over the past decade we have gained considerable experience with the analysis of nucleotide sequences. Currently, most of our effort is devoted to the analysis of next generation sequencing data that is produced in the AMC sequencing facility (Roche 454 and ABI Solid). We are involved in a large range of projects that often require the development of dedicated methods for the analysis of the data. Examples of such projects include the determination of T-cell variation, virus discovery (metagenomics), identification of alternative splicing and identification of HIV microRNAs.
 

We have developed several methods and processing pipelines for the (pre-)processing of the data:
  • Re-grouping of sequences based on one or more MIDs/barcodes, primers or other sequence tags
Revision 12
20 Dec 2009 - Main.AntoineVanKampen
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META TOPICPARENT name="SupportBioLab"
Medical Bioinformatics

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Sequence analysis
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Under construction
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Over the past decade we have gained considerable experience with the analysis of nucleotide sequences. Currently, most of our effort is devoted to the analysis of next generation sequencing data that is produced in the AMC sequencing facility (Roche 454 and ABI Solid). We are involved in a large range of projects that often require the development of dedicated methods for the analysis of the data. Examples of such projects include the determination of T-cell variation, virus discovery (metagenomics), identification of alternative splicing and identification of HIV microRNAs.
 
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If you are working at the AMC and want access to the "sequencing" section of this website, please send an e-mail to BarberaVanSchaik
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We have developed several methods and processing pipelines for the (pre-)processing of the data:
  • Re-grouping of sequences based on one or more MIDs/barcodes, primers or other sequence tags
  • Generating basic summaries about the experiments and feature counting such as exons or genes per sample
  • Identification of sequences by mapping them to reference sequences with BLAT or BLAST (e.g. against the human genome, multiple species or a custom made reference database). This generally provides the basis for downstream analysis such as gene structure determination, virus discovery, and identifying alternative splicing products.
  • Identification of patterns in the sequences (e.g. MIDs/barcodes, restriction sites, GC-content)
  • Sequence assembly of shotgun and/or paired-end reads with the Roche (Newbler) or Celera (Cabog) assembler

For specific projects that require analysis with significant computer time we make use of Grid computing.

Our web-site includes a restricted area for AMC employees with more detailed information about current sequence analysis projects, available software and infrastructure, tips & tricks, etc. If you want access to this area please contact Barbera van Schaik

For more information contact Antoine van Kampen or Barbera van Schaik
Revision 11
19 Dec 2009 - Main.AntoineVanKampen
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META TOPICPARENT name="SupportBioLab"
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Medical Bioinformatics

Sequence analysis
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Medical Bioinformatics

Back to menu

Sequence analysis
 

Under construction
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If you are working at the AMC and want access to the "sequencing" section of this website, please send an e-mail to BarberaVanSchaik \ No newline at end of file
Revision 10
18 Dec 2009 - Main.AngelaLuijf
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META TOPICPARENT name="ResearchBioLab"
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META TOPICPARENT name="SupportBioLab"
 
Medical Bioinformatics

Sequence analysis

Under construction
Revision 9
09 Dec 2009 - Main.AntoineVanKampen
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META TOPICPARENT name="ResearchBioLab"
Medical Bioinformatics

Sequence analysis
Revision 8
02 Dec 2009 - Main.BarberaVanSchaik
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META TOPICPARENT name="ResearchBioLab"
Medical Bioinformatics

Sequence analysis

Under construction
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If you are working at the AMC and want access to the "sequencing" section of this website, please send an e-mail to BarberaVanSchaik
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Revision 7
01 Dec 2009 - Main.AngelaLuijf
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META TOPICPARENT name="ResearchBioLab"
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Bioinformatics Laboratory
Medical Bioinformatics and e-Bioscience
Sequence analysis
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Medical Bioinformatics

Sequence analysis
 

Under construction
Revision 6
25 Nov 2009 - Main.BarberaVanSchaik
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META TOPICPARENT name="ResearchBioLab"
Bioinformatics Laboratory
Medical Bioinformatics and e-Bioscience
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Sequence analysis
 

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Under construction
Revision 5
16 Nov 2009 - Main.AngelaLuijf
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META TOPICPARENT name="ResearchBioLab"
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Bioinformatics Laboratory
Medical Bioinformatics and e-Bioscience
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Bioinformatics Laboratory
Medical Bioinformatics and e-Bioscience
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Revision 4
10 Nov 2009 - Main.AngelaLuijf
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META TOPICPARENT name="Trash/EducationBioLab"
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META TOPICPARENT name="ResearchBioLab"
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Medical Bioinformatics and e-Bioscience \ No newline at end of file
Revision 3
21 Sep 2009 - Main.BarberaVanSchaik
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META TOPICPARENT name="BioLab/EducationBioLab"
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META TOPICPARENT name="Trash/EducationBioLab"
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Medical Bioinformatics and e-Bioscience \ No newline at end of file
Revision 2
21 Sep 2009 - Main.BarberaVanSchaik
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META TOPICPARENT name="EducationBioLab"
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META TOPICPARENT name="BioLab/EducationBioLab"
  Bioinformatics Laboratory
Medical Bioinformatics and e-Bioscience
 
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