BOL: Related items

UCSC Genome Browser and Blat software !

Jit — Thu, 18 Feb 2016 03:18:57 -0600

This directory contains Genome Browser and Blat application binaries built for standalone
command-line use on various supported Linux and UNIX platforms. To determine which set of binaries
to download, type "uname -a" on the command line to display your machine type. In most cases the
usage statement for the application can be viewed by running the binary with no arguments.

The UCSC Genome Browser and Blat software are free for academic, nonprofit, and personal use. A
license is required for commercial download and installation of these binaries, with the exception
of items built from the following source code directories, which are freely available for all uses:

- kent/src/utils (includes big* tools)
- kent/src/lib
- kent/src/hg/autoSql
- kent/src/hg/autoXml

For information about commercial licensing of the Genome Browser software, see
http://genome.ucsc.edu/license/. The Blat and In-Silico PCR software may be commercially
licensed through Kent Informatics (http://www.kentinformatics.com).

More at http://hgdownload.cse.ucsc.edu/admin/exe/

Address of the bookmark: http://hgdownload.cse.ucsc.edu/admin/exe/

GKNO

Neel — Fri, 20 May 2016 18:56:37 -0500

gkno opens the world of complex bioinformatic analysis to people of all level of computational expertise. This site contains documentation, tutorials and information on all the tools that comprise gkno.

http://gkno.me/how-to/install.html

http://gkno.me/software.html

Address of the bookmark: http://gkno.me/

Bioinformatics tools and software

Jit — Tue, 05 Jul 2016 10:02:26 -0500

USEARCH >
Extreme high-throughput sequence analysis. Orders of magnitude faster than BLAST. MUSCLE >
Multiple sequence alignment. Faster and more accurate than CLUSTALW.

UPARSE >
OTU clustering for 16S and other marker genes. Highly accurate OTU sequences and improved diversity measures. UCHIME >
Chimeric sequence detection. PILER >
De novo genome repeat finder. PILER-CR >
Detection of CRISPR repeats in bacterial genomes. QSCORE >
Compare two multiple alignments for benchmarking. PALS >
Whole-genome alignment. PREFAB >
Protein Reference Alignment Database. MSA benchmark collection >
Selected multiple alignment benchmarks in a standardized FASTA format.

Address of the bookmark: http://drive5.com/software.html

Salzberg lab

Mon, 15 May 2017 05:14:01 -0500

We are a computational biology lab that develops novel methods for analysis of DNA and RNA sequences. Our research includes software for aligning and assembling RNA-seq data, whole-genome assembly, and microbiome analysis. We work closely with biomedical scientists to apply these methods to current problems arising in a broad spectrum of biological and medical research areas. We’re also part of the Center for Computational Biology, a group of 20+ faculty members and their labs at Johns Hopkins working on computational, statistical, and mathematical methods that can turn massive genomic data sets into biologically and clinically useful information.

https://salzberg-lab.org/

MOSS: A System for Detecting Software Similarity

Jit — Sat, 09 Dec 2017 08:59:07 -0600

Moss (for a Measure Of Software Similarity) is an automatic system for determining the similarity of programs. To date, the main application of Moss has been in detecting plagiarism in programming classes. Since its development in 1994, Moss has been very effective in this role. The algorithm behind moss is a significant improvement over other cheating detection algorithms (at least, over those known to us).

Moss can currently analyze code written in the following languages:

C, C++, Java, C#, Python, Visual Basic, Javascript, FORTRAN, ML, Haskell, Lisp, Scheme, Pascal, Modula2, Ada, Perl, TCL, Matlab, VHDL, Verilog, Spice, MIPS assembly, a8086 assembly, a8086 assembly, MIPS assembly, HCL2.

Address of the bookmark: https://theory.stanford.edu/~aiken/moss/

EvidentialGene: tr2aacds, mRNA Transcript Assembly Software

Rahul Nayak — Mon, 01 Oct 2018 13:13:24 -0500

Quality assessment of this mRNA Transcript Assembly Software is described in EvidentialGene_quality.

Too many transcript assemblies is much better than too few. It allows one then to apply biological criteria to pick out the best ones. Don't be misled by the "right number" of transcripts that one or other transcript assembler may produce. It is the "right sequence" you want, and now the only way to get it is to produce way too many assemblies on a good RNA data set, with several methods and several parameter settings.

Address of the bookmark: https://sourceforge.net/p/evidentialgene/blog/

Awesome perl frameworks, libraries and software - PART 5

Neel — Fri, 07 Jul 2017 04:12:47 -0500

robelix/sub2srt - subtitle converter
reyjrar/graphite-scripts - A Collections of Scripts for Working with Graphite
regilero/check_nginx_status - Nagios check for nginx status report
omniti-labs/resmon - resmon
motemen/App-htmlcat - redirect stdin to web browser
moose/Moo - Minimalist Object Orientation (with Moose compatibility)
miyagawa/fastpass - Tiny, XS free, standalone and preforking FastCGI daemon for PSGI
miyagawa/Filesys-Notify-Simple - Simple and dumb file system watcher
mhop/fhem-mirror - Branch 'master' is a read-only-mirror of svn://svn.code.sf.net/p/fhem/code which is updated once a day. On branch 'enocean' I am going to add some Enocean-Devices
lopnor/Plack-App-DAV - simple DAV server for Plack
kazuho/url_compress - a static PPM-based URL compressor / decompressor
jnthn/6model - Just a place that I'm keeping some meta-model prototyping; anything that matters will make it to another repo (e.g. nqp-rx one or Rakudo one) at some point.
jasonhancock/nagios-puppetdb - Nagios plugins and pnp4nagios templates related to Puppetlab's PuppetDB project.
goccy/p5-Compiler-Parser - Create Abstract Syntax Tree for Perl5
cgutteridge/Grinder - Create RDF data from spreadsheets or CSV
c9s/Plack-Middleware-OAuth - Plack Middleware for OAuth1 and OAuth2
bzip2-cuda/bzip2-cuda - Parallel implementation of bzip2 using cuda
alanstevens/ChocoPackages - Chocolatey Nuget Packages
SoylentNews/slashcode - The slashcode repository for SoylentNews. The initial code base was uploaded as it appeared on Sourceforge as of the last commit in September 2009
Miserlou/XSS-Harvest - XSS Weaponization

GenomeTools: The versatile open source genome analysis software

Jit — Wed, 07 Feb 2018 10:44:18 -0600

The GenomeTools genome analysis system is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt. It is based on a C library named “libgenometools” which consists of several modules.

If you are interested in gene prediction, have a look at GenomeThreader.

Address of the bookmark: http://genometools.org/

DECIPHER; a software toolset for deciphering and managing biological sequences efficiently using the R

BioStar — Sun, 09 Dec 2018 19:06:17 -0600

DECIPHER is a software toolset that can be used for deciphering and managing biological sequences efficiently using the R programming language. The R package is distributed as platform independent source code under the GPL version 3 license. Some functionality of the program is accessible online through web tools.

Address of the bookmark: http://www2.decipher.codes/

GenoViz: Visualization software for genomics

Rahul Nayak — Wed, 02 Jan 2019 04:07:57 -0600

GenoViz provides software applications and re-usable components for data visualization and data sharing in genomics. Our flagship product is Integrated Genome Browser (IGB).

For more information about IGB, visit http://bioviz.org.

Source code for the project was hosted here for many years. In 2014, we moved to a new git repository at http://www.bitbucket.org/lorainelab/integrated-genome-browser. We are still using SourceForge to distribute new releases of IGB as compiled code (igb.zip) you can use to run IGB on your computer.

If you have questions, feel free to get in touch. Contact project head Ann Loraine (aloraine@uncc.edu) or lead developer David Norris (dcnorris@uncc.edu>).

Address of the bookmark: https://sourceforge.net/projects/genoviz/