GenomeTraveler
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Genome Traveler is a software package developed by in silico biology, inc. in Yokohama, Japan. It is a further development of the In silico Molecular Cloning (IMC) software that has been successfully ...

Genome Traveler is a software package developed by in silico biology, inc. in Yokohama, Japan. It is a further development of the In silico Molecular Cloning (IMC) software that has been successfully introduced to the Japanese market recently. It adds state-of-the-art tools to handle and evaluate Next Generation Sequencing (NGS) data to the well-known and rich functionality inherited from the IMC packages. GeneXplain is proud to bring this program package to the international market.

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GenomeTraveler GenomeTraveler Presentation Transcript

  • NGS atgeneXplain GmbH Introducing GenomeTraveler
  • geneXplain GmbHProducts Bioinformatics and systems biology: geneXplain platform Bioinformatics and NGS: IMC and GenomeTraveler Cheminformatics: PASS, PharmaExpert, GUSAR info@genexplain.com | www.genexplain.com 2
  • Systems Biology and Cheminformatics geneXplain platform ◦ Collection, storage and analysis of experimental data ◦ Network clustering and search for master regulators ◦ Graphical programming of workflows ◦ Possibility to write new scripts and add-ons PASS and PharmaExpert ◦ Qualitative biological activity prediction for libraries of chemical compounds ◦ Drug-drug interactions and identification of most promising candidates GUSAR ◦ Quantitative biological activity prediction for libraries of chemical compounds ◦ (Q)SAR model building info@genexplain.com | www.genexplain.com 3 View slide
  • geneXplain GmbHProducts Bioinformatics and systems biology: geneXplain platform Bioinformatics and NGS: IMC and GenomeTraveler Cheminformatics: PASS, PharmaExpert, GUSAR info@genexplain.com | www.genexplain.com 4 View slide
  • Contents Primary analysis  Comparative ◦ de novo assembly genomics ◦ Scaffolding ◦ in silico cloning ◦ Mapping ◦ Genome analysis ◦ Import of mapping ◦ Array analysis results Secondary analysis  Why you should try ◦ Profile analysis GenomeTraveler ◦ Mutation analysis ◦ Expression analysis info@genexplain.com | info@genexplain.com | www.genexplain.com www.genexplain.com 5
  • Primary Analysis Getting started with NGS data info@genexplain.com | www.genexplain.com 6
  • General Information GT supports NGS data from the following sources: ◦ ABI SOLiD (CSFastA) ◦ Illumina GA (FastQ) ◦ Roche/454 GS FLX/Junior It is possible to map NGS sequences against sequence data in any of these formats: ◦ ABI/SCF ◦ GenBank ◦ FastA info@genexplain.com | www.genexplain.com 7
  • de novo Assembly de novo assembly can be done with 200 bp or larger reads, saved in the following formats: ◦ ABI/SCF/SFF/PHD ◦ FastA/FastQ/CSFastA ◦ Solexa Raw ◦ GenBank/EMBL ◦ TXT GT also supports the import of assembly files from: ◦ Velvet (AFG) ◦ Phrap (ACE) Example: assembly results imported from Phrap. info@genexplain.com | www.genexplain.com 8
  • ScaffoldingThe de novo assembly of large genomes resultsin a large number of contigs. These can becombined using paired-end short reads.Contig positions in a scaffold can be viewed inGTs "Scaffold Viewer". info@genexplain.com | www.genexplain.com 9
  • Mapping FunctionsThe mapping algorithm is based on NCBIBlast results for reference sequencescompared with NGS short reads. fragment paired-end short reads short reads multiple multiple sites chromosomes or contigs info@genexplain.com | www.genexplain.com 10
  • Import of Mapping Results GenomeTraveler can also import mapping results from other software, namely: ◦ SAMtool (SAM/BAM) ◦ SOLiD (GFF) Mapping and import results can be viewed in the "Profile and Alignment Viewer" of GT. Example: imported GFF file. info@genexplain.com | www.genexplain.com 11
  • Primary Analysis Summary Long read de novo assembly and import of Scaffolding using paired- assembly results from end short reads. Phrap and Velvet. GenomeTraveler has a number of options for the primary analysis of NGS data. Mapping: single-end, Import of mapping result paired-end, multiple files from SAMtool and chromosome/contig/site SOLiD. mapping. info@genexplain.com | www.genexplain.com 12
  • Secondary Analysis Analysis of mapped data info@genexplain.com | www.genexplain.com 13
  • General Information Once NGS data is mapped, it can be analyzed in the "Profile and Alignment Viewer". The viewer consists of four panels: ◦ Whole genome navigation panel ◦ Profile panel ◦ Genome (feature) map ◦ Sequence alignment info@genexplain.com | www.genexplain.com 14
  • Profile Analysis Peak detection can be done for one, a few or all contigs in one alignment. Peaks can be saved as CSV file or inserted as new features into the genome map. info@genexplain.com | www.genexplain.com 15
  • Mutation Analysis The "Disagreement List" is a list of bases which differ between the reference and the consensus of mapped reads (example). SNP detection ◦ Based on disagreement list ◦ Feature mapping ◦ Link generation with JSNP Indel detection info@genexplain.com | www.genexplain.com 16
  • Expression Analysis GT provides profiles and a comparison with expression profiles of tiling arrays for: ◦ RNA-Seq ◦ ChIP-Seq info@genexplain.com | www.genexplain.com 17
  • Secondary Analysis Summary Mutation analysis: find Profile analysis: detect divergent bases, SNPs and register peaks. and insertion/deletion sites. GenomeTraveler provides three fields for secondary analysis of NGS data. These are GT specific Expression analysis: GT functions that can be provides profiles for RNA- accessed in the "Profile and ChIP-Seq data. and Alignment Viewer". info@genexplain.com | www.genexplain.com 18
  • Comparative GenomicsFunctions inherited from IMC info@genexplain.com | www.genexplain.com 19
  • General InformationGenomeTraveler is basedon IMC (in silico CloningMolecular Cloning),which offers three majorin silico experimentation Genomeareas. analysisThese are also featuredin GT and can beaccessed in the "Profile Arrayand Alignment Viewer". analysis info@genexplain.com | www.genexplain.com 20
  • in silico CloningThe "Cloning" menu lists a number of possibleactions for in silico molecular cloning experiments.Included are all necessary functions for: ◦ PCR (including gel electrophoresis of results) ◦ Ligation and sequence editing ◦ Restriction enzymes and digestion (example below) info@genexplain.com | www.genexplain.com 21
  • Genome AnalysisThe "Genome Analysis" menu is filled with functions fromstatistics to visualization to working with sequences: ◦ Translation ◦ Annotation ◦ EST and trace mapping ◦ Homology searches ◦ Dot plot, Venn diagram (examples below), KEGG pathways info@genexplain.com | www.genexplain.com 22
  • Genome AnalysisThe genome rearrangement map, as partof the genome analysis functionality,compares the distribution of features onyour mapped sequence compared to anyreference sequence you set (inGenBank/EMBL/GPFF formats), as seen inthe example below. info@genexplain.com | www.genexplain.com 23
  • Array AnalysisThe "Array Analysis" menu contains all functionsnecessary for the creation and analysis of arraydata: ◦ Probe design (example below) ◦ Import of probe and array data ◦ Statistics and peak detection ◦ Two expression graphs and clustering info@genexplain.com | www.genexplain.com 24
  • Additional FunctionsThe "Profile andAlignment Viewer" hasmore to offer, though: Search for pattern matches, keywords, and more. View your sequence in different ways. Customize the genome feature map and hide the programs quick access buttons. info@genexplain.com | www.genexplain.com 25
  • Comparative Genomics Summary in silico cloning options Genome analysis include PCR, restriction features translation, and ligation of annotation, homology sequences. searches and more. With GenomeTraveler you can work in silico with your NGS data. Array analysis offers The additional functions probe design, data of the "Profile and import, peak detection Alignment Viewer" render and more. GT more flexible. info@genexplain.com | www.genexplain.com 26
  • Why You ShouldTry GenomeTraveler Advantages of the Software info@genexplain.com | www.genexplain.com 27
  • Key Notes GenomeTraveler has a number of options for the primary analysis of NGS data. GenomeTraveler provides three fields for secondary analysis of NGS data. With GenomeTraveler you can work in silico with your NGS data. You can download a free two-week trial version of GenomeTraveler at http://www.genexplain.com/genome-traveler info@genexplain.com | www.genexplain.com 28