Results for "graph-based"
Blogs
Five unique traits of effective computational biologist
Bioinformatics research is driven by large set of software, scripts, and tools to analyse gigantic biological data. Being a great biological programmer or bioinformaticia...3962 days ago
Five points for bioinformatics software/tools
In the bioinformatics sector we mostly spend time on computational analysis of huge amounts of data and try to make sense of it, biologically. But, most of the newbie bio...3719 days ago
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Bookmarks
Well designed regular expression cheat sheet
In our computational biology work, we mostly play with DNA or AA string. For string based programming work this regular expression cheat sheet is really helpful. Keep it handy.3961 days ago
DAVI: Deep learning-based tool for alignment and single nucleotide variant identification
DAVI consists of models for both global and local alignment and for variant calling. We have evaluated the performance of DAVI against existing state-of-the-art tool sets...1157 days ago
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Files
Master Thesis: Trans-membrane topology prediction through Markov based decoders
Abstract: Background/Motivation: The dearth of structural information on alpha helical membrane protein (MPs) has hindered thus far the development of reliable knowled...3956 days ago
Evaluation of genome assembly software based on long reads
TGS technologies have been used to produce highly accurate de novo assemblies of hundreds of microbial genomes and highly contiguous reconstructions of many dozens of pla...1931 days ago
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Discussion topics
Which are the best statistical programming languages to study for a bioinformatician?
In Bio-informatics based genome sequencing and predicting metabolic pathways research jobs I used Matlab, SAS, SPSS, R and several Bioconductor packages. M...3963 days ago
Pages
Bio++ : C Language libraries for your biological need
C has always been a language that never attempts to tie a programmer down - it allows for easy implementation, it comes with a genuinely useful standard library that can...3959 days ago
- I found several useful bioinformatics articles which exaplain, define and elaborate the bioinformatics in scientific way. Therefore, instead of writting it again I d...
3932 days ago
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Top-level pages
- "Bioinformatics is a science of biological predictions and analysis" -- Jitendra Narayan "The mathematical, statistical and computing methods that aim to solve biol...
3959 days ago
- Data mining, the extraction of hidden predictive information from large databases. Data mining is becoming an increasingly important tool to transform this data into info...
3958 days ago
- +45 more Top-level pages
Wire posts
News
- This pdf based tutorial in good resource to understand the basic of Perl in a day http://ritg.med.harvard.edu/training/perl/RC_Perl_Intro.pdf
3932 days ago
Webinar: Wednesday 21 August 2013 at Noon EDT
This webinar will describe the use of combinatorial pooling to reconstruct gene sequences within BACs. Recent work in barley has shown that this level of sequence knowled...3931 days ago
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Opportunity posts
- van Noort Group is looking for PhD fellows We currently access an unprecedented knowledge on the basic components making up living systems. An ever growing number of n...
3960 days ago
- At TU Dresden, Faculty of Computer Science, the DFG Research Training Group GRK 1907 “Role-based Software Infrastructures for continuous-context-sensitive Systems” offers...
3959 days ago
- +118 more Opportunity posts
ResearchLabs posts
The Centre for Bioinformatics, Biomarker Discovery and Information-Based Medicine (CIBM)
The Centre for Bioinformatics, Biomarker Discovery and Information-Based Medicine (CIBM) is committed to shortening the process of obtaining novel discoveries to achieve...3959 days ago
- Infectious disease control needs to be made more “sustainable”. We need to reduce selective pressure on pathogens to evolve antibiotic resistance. We need to control infe...
3959 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 Air date: Wednesday, February 01, 2012, 3:00:00 PM Category: Wednesday Afternoon Le...3913 days ago
Spotlight on Genomics: Understanding Our Genes - A Step to Personalized Medicine
(Visit: http://www.uctv.tv/) Learn about the essential role of genomics in the development of stem cell based therapies. Craig Venter, president and founder of the J. Cra...3916 days ago
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Bio-Scripts
Extracting FASTA sequences based on position with perl script !!
#!/usr/bin/env perl #Uses: perl sub-seq.pl input.txt range use strict; use warnings; my $end = pop; my $start = pop; local $/ = '>'; while () {...2633 days ago
- # 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
2276 days ago
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Tryst
Tryst with a Bioinformatician # Dr Altan Kara
Dr Altan Kara is a Bioinformatics specialist at the faculty of Gene Engineering and Biotechnology Institute at TUBITAK MAM Research Center. His research interest...2373 days ago
Groups
Web prgramming for biologist/bioinformatician
PHP is quite popular these days (in combination with mySQL (query and design db), CSS (for styling) and HTML) for web programming and online database management for publi...3647 days ago
Tags
NextDenovo: string graph-based de novo assembler for TGS long reads
NextDenovo is a string graph-based de novo assembler for TGS long reads. It uses a "correct-then-assemble" strategy similar to canu, but requires significantly less computing resources and storages. After assembly, the per-base error rate is about 97-98%, to further improve single base ...Tags: NextDenovo, NextOmics, string, graph-based, de novo, assembler, TGS, LongReads, assembly, long, reads
1594 days ago
Comments
Comment on "Sibelia: A comparative genomics tool"
Basic usage =========== In this manual it is assumed that "Sibelia" is properly installed and the directory with "Sibelia.py" is in your "PATH" environment variable or...1296 days ago
Comment on "KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies"
Using KAT again (You will need the modules: KAT/2.1.1 and gnuplot/4.6.5) – we can plot the kmer content of the assembly compared to the kmer content...1348 days ago
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