BOL: Related items

xmatchview: smith-waterman alignment visualization

Rahul Nayak — Thu, 28 Dec 2017 09:00:58 -0600

xmatchview and xmatchview-conifer are imaging tools for comparing the synteny between DNA sequences. It allows users to align 2 DNA sequences in fasta format using cross_match and displays the alignment in a variety of image formats. xmatchview and xmatchview-conifer are written in python and run on linux and windows. They serve as visual tools for analyzing cross_match alignments. Cross_match (Green, P. (1994) http://www.phrap.org) uses an implementation of the Smith-Waterman algorithm for comparing DNA sequences that is sensitive.

http://www.bcgsc.ca/platform/bioinfo/software/xmatchview

Address of the bookmark: https://github.com/warrenlr/xmatchview

Sibelia: A comparative genomics tool

BioStar — Sat, 22 Aug 2020 02:49:00 -0500

Sibelia: A comparative genomics tool: It assists biologists in analysing the genomic variations that correlate with pathogens, or the genomic changes that help microorganisms adapt in different environments. Sibelia will also be helpful for the evolutionary and genome rearrangement studies for multiple strains of microorganisms.

Sibelia is useful in finding: (1) shared regions, (2) regions that present in one group of genomes but not in others, (3) rearrangements that transform one genome to other genomes.

More at http://bioinf.spbau.ru/sibelia

Sibelia docs http://gensoft.pasteur.fr/docs/Sibelia/3.0.7/SIBELIA.md

Address of the bookmark: https://github.com/bioinf/Sibelia

Synorth: exploring the evolution of synteny and long-range regulatory interactions in vertebrate genomes

LEGE — Mon, 06 May 2024 06:21:10 -0500

Genomic regulatory blocks are chromosomal regions spanned by long clusters of highly conserved noncoding elements devoted to long-range regulation of developmental genes, often immobilizing other, unrelated genes into long-lasting syntenic arrangements. Synorth http://synorth.genereg.net/ is a web resource for exploring and categorizing the syntenic relationships in genomic regulatory blocks across multiple genomes, tracing their evolutionary fate after teleost whole genome duplication at the level of genomic regulatory block loci, individual genes, and their phylogenetic context.

More at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2745767/

Address of the bookmark: http://synorth.genereg.net/

GTDB-Tk: A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

Rahul Nayak — Wed, 22 Aug 2018 03:21:01 -0500

GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes. It is computationally efficient and designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3).

GTDB-Tk is under active development and validation. Please independently confirm the GTDB-Tk predictions by manually inspecting the tree and bringing any discrepencies to our attention. Notifications about GTDB-Tk releases will be available through the ACE Twitter account (https://twitter.com/ace_uq).

Address of the bookmark: https://github.com/Ecogenomics/GTDBTk

‘dockr’: the R container

Jit — Mon, 23 Dec 2019 09:56:49 -0600

dockr 0.8.6 is now available on CRAN. dockr is a minimal toolkit to build a lightweight Docker container image for your R package, in which the package itself is available. The Docker image seeks to mirror your R session as close as possible with respect to R specific dependencies. Both dependencies on CRAN R packages as well as local non-CRAN R packages will be included in the Docker container image.

If you want to know, how Docker works, and why you should consider using Docker, please take a look at the Docker website.

Address of the bookmark: https://www.docker.com/why-docker

LIBSVM -- A Library for Support Vector Machines

Neel — Wed, 02 Aug 2017 06:49:05 -0500

LIBSVM is an integrated software for support vector classification, (C-SVC, nu-SVC), regression (epsilon-SVR, nu-SVR) and distribution estimation (one-class SVM). It supports multi-class classification.

Since version 2.8, it implements an SMO-type algorithm proposed in this paper:
R.-E. Fan, P.-H. Chen, and C.-J. Lin. Working set selection using second order information for training SVM. Journal of Machine Learning Research 6, 1889-1918, 2005. You can also find a pseudo code there. (how to cite LIBSVM)

Our goal is to help users from other fields to easily use SVM as a tool. LIBSVM provides a simple interface where users can easily link it with their own programs. Main features of LIBSVM include

Different SVM formulations
Efficient multi-class classification
Cross validation for model selection
Probability estimates
Various kernels (including precomputed kernel matrix)
Weighted SVM for unbalanced data
Both C++ and Java sources
GUI demonstrating SVM classification and regression
Python, R, MATLAB, Perl, Ruby, Weka, Common LISP, CLISP, Haskell, OCaml, LabVIEW, and PHP interfaces. C# .NET code and CUDA extension is available.
It's also included in some data mining environments: RapidMiner, PCP, and LIONsolver.
Automatic model selection which can generate contour of cross validation accuracy.

https://www.csie.ntu.edu.tw/~cjlin/libsvm/

Address of the bookmark: https://www.csie.ntu.edu.tw/~cjlin/libsvm/

InteractiVenn: a web-based tool for the analysis of sets through Venn diagrams

Jit — Wed, 29 Jun 2022 03:22:26 -0500

InteractiVenn, a more flexible tool for interacting with Venn diagrams including up to six sets. It offers a clean interface for Venn diagram construction and enables analysis of set unions while preserving the shape of the diagram. Set unions are useful to reveal differences and similarities among sets and may be guided in our tool by a tree or by a list of set unions. The tool also allows obtaining subsets’ elements, saving and loading sets for further analyses, and exporting the diagram in vector and image formats. InteractiVenn has been used to analyze two biological datasets, but it may serve set analysis in a broad range of domains.

More at https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0611-3

Address of the bookmark: http://www.interactivenn.net/