Results for "seed-and-extension-based"
Blogs
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 bioinforma...3720 days ago
List of bioinformatics workflow management tools !
Here are list of Workflow Managers BigDataScript – A cross-system scripting language for working with big data pipelines in computer systems of different size...1155 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.3963 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 and fo...1159 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 knowledge &nda...3958 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 plant and...1933 days ago
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. Matlab h...3965 days ago
- I'm new to bioinformatics and recently started learning Perl. I found several rival distributions available for Windows platform, which confuse me at the begining. I google it...
3928 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 itself...3960 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 decided...
3934 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 biological...
3960 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 information...
3959 days ago
- +47 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
3933 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 knowledge is s...3932 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 new tech...
3961 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 the po...
3961 days ago
- +124 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 distinc...3961 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 infectious...
3961 days ago
- +11 more ResearchLabs posts
Video
- http:--www.biotechnology.jhu.edu- Tutorial for PSI-BLAST, an extension of BLAST that uses matrix algebra. BLAST is a cornerstone bioinformatics tool at NCBI. BLAST is the Basic Local Alignment Search tool and will protein and DNA sequences that are related to a sequence that the user provides.
3921 days ago
Bioinformatics 101 - Running BLAST
How to format the database for BLAST, run the command, view the output file, and use BioPerl and Perl to parse the output. By David Francis, Ohio State University. Delivered liv...3910 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 () { chomp;...2634 days ago
Download the genome from NCBI using bash script/command
#!/bin/bash # Download the genome from NCBI using command # Create a Directory mkdir genome cd genome # Look for genome assembly summary and extract the URL # USER n...2545 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 revolve...2375 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 publishing h...3649 days ago
Tags
rHAT: a seed-and-extension-based noisy long read alignment tool
rHAT is a seed-and-extension-based noisy long read alignment tool. It is suitable for aligning 3rd generation sequencing reads which are in large read length with relatively high error rate, especially Pacbio's Single Molecule Read-time (SMRT) sequencing reads.Tags: rHAT, seed-and-extension-based, noisy, long, read, alignment, tool, ont, pacbio
2064 days ago
Comments
Comment on "LAMSA: fast split read alignment with long approximate matches"
➜ LAMSA git:(master) ./lamsa aln Usage: lamsa aln [options] <ref.fa> <read.fa/fq> Algorithm options: -t --thread [INT] Number of threads. [1] -l --seed-len [INT]...2135 days ago
- Platanus README ***** VERSION ***** 1.2.3 ***** DESCRIPTION ***** Platanus is a de novo assembler designed to assemble high-throughput data. It can handle highly h...
2812 days ago
