Results for "Overlap Graph"
Blogs
Five unique traits of effective computational biologist
Bioinformatics research is driven by large set of software, scripts, and tools to anal...r to interact with biotech researchers and learn how do they explain their one graph (which they generally produce...3940 days ago
Five points for bioinformatics software/tools
In the bioinformatics sector we mostly spend time on computational analysis of huge am...at you need in your analysis is already coded into the program. Need to plot a graph? Just click this button right...3697 days ago
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Bookmarks
InfoGenomeR: Integrative reconstruction of cancer genome karyotypes
InfoGenomeR is the Integrative Framework for Genome Reconstruction that uses a breakpoint graph to model the connectivity amo...type information to identify the optimal breakpoint graph representing cancer genomes....1086 days ago
RNA-Seq De novo Assembly Using Trinity
Trinity, developed at the Broad Institute and...e data into many individual de Bruijn graphs, each representing the trans...ene or locus, and then processes each graph independently to extract full...ers and constructs complete de Bruijn graphs for each cluster. Each clust...2955 days ago
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Files
R Graphical Cookbook by Winston Chang
R Graphical Cookbook by Winston Chang A very nice book by Winston Chang for R ethusiast. The R code presented in th...roduce the figure is included. This means that there is sometimes considerable overlap...2144 days ago
Prepare for Coding Interview !
This is a comprehensive guide to prepare for your next coding interview. It's great fo...view_experience_at_google/ #bottom-comments. 1. Data structures 2. Trees and Graph algorithms 3. Dynamic Progra...835 days ago
Pages
Genome Assembly Tools and Software - PART2 !!
...ories: string-based model and graph-based model. We therefore list...scovery. SAGE – String Graph Assembly of GEnomesSAGE is a new string-overlap graph-based de novo genome as...to obtain all sequences that overlaps, directly or indirectly, w...2675 days ago
Awesome perl frameworks, libraries and software - PART 2
licheng/gccfilter - gccfilter is a per...l-GD - Perl GD module for bitmap graphics keiya/KeiSpade-CMS -...n terms of AnyEvent agentzh/makefile-graphviz-pm - Perl CPAN module...nbsp;- MySQL stats logging for Statsd/Graphite naoya/hadoop-streaming-fr...2484 days ago
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Top-level pages
- Data mining, the extraction of hidden predictive informatio...t be your strong point. Excel is fine for creating graphs. If you’re serious abo...age informatics and scalable querying and mining of graphs.For more detail visit: ...
3936 days ago
- ...programming The shortest path in a weighted graph can be found by using the short...ndependent in divide and conquer, where as the overlap of subproblems occur in dyn...problems such as the maximum flow for directed graphs, notably by using the simple...
3936 days ago
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Wire posts
News
BEReX : Biomedical Entity-Relation eXplorer
BEReX is a new biomedical knowledge integration, search, and exploration tool. BEReX i...keywords and BEReX returns a sub-network matching the keywords. The resulting graph can be explored interactively...3829 days ago
- A team from Cold Spring Harbor Laboratory has released an algorithm, called Scalpel, f...(including partial matches), splits them into k-mers, and creates a de Bruijn graph to span the exon; however, if...
3536 days ago
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Opportunity posts
Post-doc position at LABGeM - Evry, France
The LABGeM team (CEA/Genoscope, CNRS UMR 8030, France, Dir. Claudine Médigue) is devel...nd enzyme families. These methods will be based on protein family analysis and graph approaches combining genomic...3058 days ago
11th International Joint Conference on Biomedical Engineering Systems and Technologies
BIOSTEC, the 11th International Joint Conference on Biomedical Engineering Systems and...systems biology, sequence analysis, biostatistics, image analysis, network and graph models, scientific data manag...2639 days ago
ResearchLabs posts
- Nataša Pržulj Lab's research involves applications of graph theory, mathematical modeling, and computational techniques to solving large-scale problems in computational and systems biology.They...
3891 days ago
- Genome sequencing projects have enormous potential for benefiting human endeavors. However, just as acquiring a lang...n. In such cases functionally similar proteins may have less than 25% sequence overl...
3875 days ago
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Video
Computational Biology in the 21st Century: Making Sense out of Massive Data
Computational Biology in the 21st Century: Making Sense out of Massive Data A...algorithms. We show how ideas from cutting-edge algorithms, including spectral graph theory and modern data struct...3892 days ago
Bio-Scripts
- # Count k-mer occurrence using Jellyfish 2.2.6 jellyfish count -t 8 -C -m 19 -s 5G -o 19mer_out --min-qual-char=? sread_1.fastq sread_2.fastq # points for a histogram jellyfish histo -o 19mer_out.histo 19mer_out #Plot results using R ##load the data into dataframe19 dataframe19
2254 days ago
Estimate Genome Size with Jellyfish and R
jellyfish count -t 8 -C -m 19 -s 5G -o 19mer_out --min-qual-char=? /common/Tutorial/Genome_estimation/sample_read_1.fastq /common/Tutorial/Genome_estimation/sample_rea...2236 days ago
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Tags
CABOG: Celera Assembler with Best Overlap Graph
CABOG (Celera Assembler with Best Overlap Graph) is scientific software for DNA research. CABOG has been a critical component of many genome sequencing projects. CABOG operates on small genomes such as bacterial as well as large genomes such as mammalian. CABOG is an extension of the Celera ...Tags: CABOG, Celera, Assembler, Overlap Graph, Bioinformatics, Assembly, Genome, Reads, NGS
2537 days ago
Comments
Comment on "GraphMap - A highly sensitive and accurate mapper for long, error-prone reads"
urbe@urbo214b[genome] graphmap align -h []GraphMap - A very accurate and sensit...SAM output (in normal and '-w overlap' modes). m5 - BLASR M5 form...w normal -M 5 -X 4 -G 8 -E 6' overlap - Equivalent to: '-a anchor...Algorithmic options: -k INT Graph construction kmer size. [6] -...2282 days ago
- ...the algorithm based on de Bruijn graph. Second, the order of contigs i...the algorithm based on de Bruign graph. INPUT OPTIONS...eed. -v INT : Minimum overlap length (default 32)...If adjacent contigs have overlap (length >= INT) and prop...
2789 days ago
