Results for "pre-alignment"
Blogs
XAMPP: Starting Apache fail Ubuntu
Once you install XAMMP on linux, the most common problem you face is Apache failure. To fix the issues please use following command to first stop and then again start it....3634 days ago
Computer simulation of genetic mechanism !!
Computer simulation is the discipline of designing a model of an actual or theoretical physical/biological system, executing the model on a digital computer, and analyzing...2990 days ago
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Bookmarks
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...1161 days ago
Nucl2Vec: Local alignment of DNA sequences using Distributed Vector Representation
We demonstrate a novel approach forlocal alignment of DNA reads with respect to reference genome.For this process we have used Skip-gram model for creatingencoding(Nucl2Ve...1161 days ago
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Files
Bioinformatics approach to Boar Taint
Meat products obtained from intact male pigs often produce offensive smell or odour which is recognized as a complex genetic trait called boar taint.Androstenone and Skato...3804 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 i...3962 days ago
BioRuby :Ruby packages for biologist
BioRuby is a package of Open Source Ruby code, with classes for DNA and protein sequence analysis, alignment, database parsing, and other Bioinformatics tools.BioRuby proj...3962 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 biolo...
3962 days ago
- An algorithm is a computable set of steps to achieve a desired result. We use algorithms every day. For example, a recipe for baking a cake is an algorithm. Most programs...
3961 days ago
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Wire posts
News
- PhylomeDB is a public database for complete collections of gene phylogenies (phylomes). It allows users to interactively explore the evolutionary history of gene...
3934 days ago
Update Genome Workbench 2.7.15 released
NCBI Genome Workbench is an integrated application for viewing and analyzing sequence data. With Genome Workbench, you can view data in publically available sequence datab...3735 days ago
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Opportunity posts
Clinical Genomics & Informatics Europe at Lisbon, Portugal
Bio-IT World and Cambridge Healthtech Institute's fifth international Clinical Genomics & Informatics Europe conference will feature four main tracks on Clinical Exome...3932 days ago
Pre- or postdoctoral research fellowship in Structural Bioinformatics in Padova
University of Padova (URL: http://protein.bio.unipd.it/) A research fellowship is available at the BioComputing Laboratory, University of Padova (URL: http://protein.bi...3883 days ago
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ResearchLabs posts
The Laboratoire de genomique fonctionelle
One persistent challenge of post genome biology remains the determination of the functions of all potential genes. In mammals this task is formidable given that a single g...3963 days ago
- Raphael Lab research is focused on Bioinformatics and Computational Biology. Current research interests include next-generation DNA sequencing, structural variation, ge...
3242 days ago
Fun
Bioinformatician become producer/director !!!
If a Bioinformatician starts producing Hindi Bollywood movies, names will be like this.... BLAST : Eak khoj Munna Bhai Promoter Gene se Genome tak. Maine BLAST kiya....3933 days ago
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.
3923 days ago
- lecture 9, Chem. C100, Spring 2013, UCLA
3924 days ago
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Bio-Scripts
Download genome using NCBI esearch command line !
#Download using command line "NC_005956.1" / "CP003784.1" esearch -db nucleotide -query "NC_005956.1" | efetch -format fasta > seq1.fa esearch -db nucleotide -query "...1116 days ago
Blast result parser with Perl and Bioperl
#!/usr/local/bin/perl # # Dr. Xiaodong Bai # It may be freely distributed under GNU General Public License. # This script will parse a NCBI blastx output file and ou...2929 days ago
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Groups
Ruby is a dynamic, reflective, general-purpose object-oriented programming language that combines syntax inspired by Perl with Smalltalk-like features. It was also influen...3935 days ago
Metabolomics is the comprehensive and quantitative analysis of multiple metabolites in biological samples. Metabolome is the complete set of small-molecule metabolites f...3720 days ago
Tags
Shouji: a fast and efficient pre-alignment filter for sequence alignment
The ability to generate massive amounts of sequencing data continues to overwhelm the processing capacity of existing algorithms and compute infrastructures. In this work, we explore the use of hardware/software co-design and hardware acceleration to significantly reduce the execution time of sho...Tags: Shouji, fast, efficient, pre-alignment, filter, sequence, alignment
1659 days ago
SneakySnake: A Fast and Accurate Universal Genome Pre-Alignment Filter for CPUs, GPUs, and FPGAs
The first and the only pre-alignment filtering algorithm that works efficiently and fast on modern CPU, FPGA, and GPU architectures. SneakySnake greatly (by more than two orders of magnitude) expedites sequence alignment calculation for both short (Illumina) and long (ONT and PacBio) reads. Descr...Tags: SneakySnake, Fast, Accurate, Universal, Genome, Pre-Alignment, Filter, CPUs, GPUs, FPGAs
1247 days ago
Comments
Comment on "How to install Perl modules manually, using CPAN command, and other quick ways"
Installing in CONDA env You can check using which perl - it should give you the perl that's located within your conda environment. In this case, it should...431 days ago
Comment on "Elgg Installation steps !"
If you need to uninstall all MySQL packages sudo apt-get remove --purge mysql* sudo apt-get autoremove sudo apt-get autoclean440 days ago
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