BOL: Related items

Machine learning in Perl

Jit — Sun, 16 Feb 2020 15:32:03 -0600

this is a fourth blog post in the Machine learning in Perl series, focusing on the AI::MXNet, a Perl interface to Apache MXNet, a modern and powerful machine learning library.

If you're interested in refreshing your memory or just new to the series, please check previous entries over here: 1 2 3

https://metacpan.org/pod/AI::MXNet

Address of the bookmark: http://blogs.perl.org/users/sergey_kolychev/2018/07/machine-learning-in-perl-kyuubi-goes-to-a-modelzoo-during-the-starry-night.html

Download mutliple fasta file from NCBI in one GO!!

Rahul Agarwal — Wed, 21 Aug 2013 08:13:30 -0500

if you have less time, then use three ways mentioned in bookmark link to extract/download all fasta sequences in single click given that you already have a list of GIs or accession IDs .

Alternatively, use one liner perl script:

perl -ne 'if(/^>(\S+)/){$c=$i{$1}}$c?print:chomp;$i{$_}=1 if @ARGV' GIs.txt >sequence.fasta

where GIs.txt contains a list of GIs or accession IDs.

(from :http://edwards.sdsu.edu/labsite/index.php/robert?start=5)

Address of the bookmark: http://edwards.sdsu.edu/labsite/index.php/robert/380-ncbi-sequence-or-fasta-batch-download-using-entrez

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

TwinBLAST: When Two Is Better than One

Jit — Sat, 07 Sep 2019 08:50:08 -0500

TwinBLAST is a web-based tool for viewing 2 BLAST reports simultaneouslyside-by-side. It uses ExtJS (www.sencha.com/products/extjs/) to provide 2independently scrollable panels. BioPerl (www.bioperl.org) is used to indexraw BLAST reports and Bio::Graphics is used to draw pictograms of the BLASThits.

https://github.com/IGS/twinblast

https://mra.asm.org/content/8/35/e00842-19

Address of the bookmark: https://github.com/IGS/twinblast

Recombination detection tool

Jit — Tue, 02 Feb 2016 10:11:14 -0600

A program to detect recombination hotspots using population genetic data.

More at https://github.com/auton1/LDhot

Address of the bookmark: https://github.com/auton1/LDhot

RASTtk : algorithm for building custom annotation pipelines and annotating batches of genomes

Abhi — Wed, 27 Apr 2016 11:07:59 -0500

The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard software pipeline for identifying genomic features (i.e., protein-encoding genes and RNA) and annotating their functions. Recently, in order to make RAST a more useful research tool and to keep pace with advancements in bioinformatics, it has become desirable to build a version of RAST that is both customizable and extensible. In this paper, we describe the RAST tool kit (RASTtk), a modular version of RAST that enables researchers to build custom annotation pipelines. RASTtk offers a choice of software for identifying and annotating genomic features as well as the ability to add custom features to an annotation job. RASTtk also accommodates the batch submission of genomes and the ability to customize annotation protocols for batch submissions. This is the first major software restructuring of RAST since its inception.

More at http://www.nature.com/articles/srep08365

Address of the bookmark: http://rast.nmpdr.org/

MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping

Neel — Fri, 20 May 2016 18:53:49 -0500

MOSAIK is a stable, sensitive and open-source program for mapping second and third-generation sequencing reads to a reference genome. Uniquely among current mapping tools, MOSAIK can align reads generated by all the major sequencing technologies, including Illumina, Applied Biosystems SOLiD, Roche 454, Ion Torrent and Pacific BioSciences SMRT. Indeed, MOSAIK was the only aligner to provide consistent mappings for all the generated data (sequencing technologies, low-coverage and exome) in the 1000 Genomes Project. To provide highly accurate alignments, MOSAIK employs a hash clustering strategy coupled with the Smith-Waterman algorithm. This method is well-suited to capture mismatches as well as short insertions and deletions. To support the growing interest in larger structural variant (SV) discovery, MOSAIK provides explicit support for handling known-sequence SVs, e.g. mobile element insertions (MEIs) as well as generating outputs tailored to aid in SV discovery.

Address of the bookmark: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0090581

GAEMR

Jit — Tue, 14 Jun 2016 06:18:37 -0500

The Genome Assembly Evaluation Metrics and Reporting (GAEMR) package is an assembly analysis framework composed a number of integrated modules. These modules can be executed as a single program to generate a complete analysis report, or executed individually to generate specific charts and tables. GAEMR standardizes input by converting a variety of read types to Binary Alignment Map (BAM) format, allowing a single input format to be entered into GAEMR’s analysis pipeline, hence enabling the generation of standard reports.

GAEMR’s analysis philosophy is centered on contiguity, correctness, and completeness -- how many pieces in an assembly composed of, how well those pieces accurately represent the genome sequenced, and how much of that genome is represented by those pieces. By performing over twenty different analyses based on these principles, GAEMR gives a clear picture of the condition of a genome assembly.

Address of the bookmark: https://www.broadinstitute.org/software/gaemr/

Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm)

Abhimanyu Singh — Thu, 29 Dec 2016 03:26:45 -0600

Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee. Key features of Prodigal include:

Speed: Prodigal is an extremely fast gene recognition tool (written in very vanilla C). It can analyze an entire microbial genome in 30 seconds or less.
Accuracy: Prodigal is a highly accurate gene finder. It correctly locates the 3' end of every gene in the experimentally verified Ecogene data set (except those containing introns). It possesses a very sophisticated ribosomal binding site scoring system that enables it to locate the translation initiation site with great accuracy (96% of the 5' ends in the Ecogene data set are located correctly).
Specificity: Prodigal's false positive rate compares favorably with other gene identification programs, and usually falls under 5%.
GC-Content Indifferent: Prodigal performs well even in high GC genomes, with over a 90% perfect match (5'+3') to the Pseudomonas aeruginosa curated annotations.
Metagenomic Version: Prodigal can run in metagenomic mode and analyze sequences even when the organism is unknown.
Ease of Use: Prodigal can be run in one step on a single genomic sequence or on a draft genome containing many sequences. It does not need to be supplied with any knowledge of the organism, as it learns all the properties it needs to on its own.
Open Source: Prodigal source code is freely available under the General Public License.

Download the latest version of Prodigal at the Prodigal github page.
or
Browse the wiki documenation.

Address of the bookmark: http://prodigal.ornl.gov/

maf2synteny

Abhimanyu Singh — Thu, 18 May 2017 05:31:30 -0500

A tool for converting for recovering synteny blocks from multiple alignment (in MAF fromat)

This tool is a standalone version of Ragout module [http://fenderglass.github./Ragout]

Address of the bookmark: https://github.com/fenderglass/maf2synteny