Results for "BED files"
Blogs
In comparative genome analysis work, we...Mac OS1. SetupCreate a folder for the files:$ mkdir -p /SourceCache$ cd /...n.org/~lds/GD-2.46/)Place the "tar.gz" files in "/SourceCache" and double...sed this was because of some left over files from the failed build. I don&...3930 days ago
Tools to detect synteny blocks regions among multiple genomes
The synteny block (which etymologically means “on....php) Genome Synteny Viewer allows users to upload files which contain synteny regions...en them. GSV also allows users to upload annotation files to visualize annotated region...2601 days ago
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Bookmarks
Latest paper on comparison of mapping tools
A. Hatem, D. Bozdag, A. E. Toland, U. V. Catalyurek "Benchmarking short sequence ma...T http://mrsfast.sourceforge.net/Home http://sourceforge.net/projects/mrsfast/files/mrsfast-ultra-3.1.0/ BFAST...3887 days ago
Public Databases for Bioinformatics !
...12TB RAID5 local storage Filesystem: /users/$USER defa...atterns: # gzip a bunch of files parallel gzip -- *.FILESTO...https://www.encodeproject.org/files/ENCFF446WOD/@@download/ENCFF446WOD.bed.gz, https://www.encodeproj...sts/hg38-human/hg38.blacklist.bed.gz. The human genome version hg...1130 days ago
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Files
Prepare for Coding Interview !
This is a comprehensive guide to prepare for your next coding interview. It's great...ive algorithms 5. Scheduling algorithms (Greedy) 6. Caching 1 7. Sorting 8. Files 9. Computability 10. Bitwis...836 days ago
Pages
Bio++ : C Language libraries for your biological need
C has always been a language that never attempts to tie...structure and IO Phylogenetic trees.IO from newick files, with support for multiple en...simony (NNI)Distance matrices estimation and I/O to files in Phylip format.Distance met...3938 days ago
BioRuby :Ruby packages for biologist
BioRuby is a package of Open Source Ruby code, with classes for DNA and protein seq...as started in late 2000, and is still in progress. Currently, there are over 80 files and 15,000 lines (except comm...3938 days ago
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Top-level pages
- Genomics is the study of the genomes of organisms. The field includes...ranslation. Chromas It will display and prints chromatogram files from ABI automated DNA sequencers, and Staden SCF files which the analysis programs f...
3933 days ago
Bioinformatics Courses Around the World
Bioinformatics Courses around the world Here is the list Bioinformatics courses offered around the world. Reasons for constructing this page are: To show the exten...3934 days ago
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Wire posts
News
Programming language to build synthetic DNA
A team led by Georg Seelig (http://homes.cs.washington.edu/~seelig/index.html) at University of Washing...hat can guide the behavior of chemical-reaction mixtures in the same way that embedde...3860 days ago
Biggest Human Brain Project (HBP) launched!!!
"In neuroscience, the project will use neuroinformatics and brain simulation to collect and integrate experimental data, identifying and filling gaps in our knowledg...3852 days ago
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Opportunity posts
Postdoctoral Associate - Bioinformatics at Duke University Medical Center
The Department of Biostatistics and Bioinformatics at Duke University Medical Cente...stat.duke.edu. For more info: http://biostat.duke.edu/sites/biostat.duke.edu/files/Halabi%20-%20Postdoc%20Job%20...3911 days ago
CSIR-INSTITUTE OF GENOMICS & INTEGRATIVE BIOLOGY
CSIR-INSTITUTE OF GENOMICS & INTEGRATIVE BIOLOGY, Mall Road, Delhi 110007 PO...ntry will be closed by 10:00 AM. More @ http://www.igib.res.in/sites/default/files/23092013.htm3893 days ago
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Bio-Scripts
Python script to download covid genome !
#!/usr/bin/env python3 # these are the publicly available "complete" sequences...seqs = yaml.load(requests.get("https://www.ncbi.nlm.nih.gov/core/assets/genbank/files/ncov-sequences.yaml").text)...1127 days ago
Install BLAST in Ubuntu/Linux and Window !
#On ubuntu sudo apt-get install ncbi-blast+ #Ubuntu Conda installation conda...#Run this installer using the defaults, it should put BLAST under C:\Program Files\NCBI\blast-2.7.1+...1137 days ago
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Tryst
Tryst with a Bioinformatician # Dr Altan Kara
Dr Altan Kara is a Bioinformatics specialist at...in the gene, transcript, protein, and metabolite profiles between normal tissue, normal...ays easily control input output directories, modify files or directories, annotate and...2353 days ago
Tags
Using Interval Trees to Query Genome Annotations by Position
To work on query related to overlapping genomic features: use IntervalTree python pkg http://informatics.malariagen.net/2011/07/07/using-interval-trees-to-query-genome-annotations-by-position/ http://hackmap.blogspot.de/2008/11/python-interval-tree.html http://en.wikipedia.org/wiki/Interval_tr...Tags: genome overlapping features, BED files, IntervalTrees
3540 days ago
Comments
Comment on "Genome in a Bottle (GIAB) Consortium"
...echnologies to generate variant calls and regions for use in benchmarking and validating variant calling pipelines. Currently, benchmark VCF and BED files for small variants are availa...1550 days ago
- ...of data is possible from FastQfiles, BAM or SAM format. This to...The input could be one or more BAM files. HTML reports are generated a...The input can be SAM, BAM, FASTA, BED files or Chromosome size file (...lation positions for RRBS sequence files (for directional, non-directi...
2128 days ago
