BOL: Related items

SMASH: An alignment-free tool to find and visualise rearrangements between pairs of DNA sequences

Jit — Thu, 21 Dec 2017 08:26:57 -0600

SMASH is a completely alignment-free method to find and visualise rearrangements between pairs of DNA sequences. The detection is based on relative compression, namely using a FCM, also known as Markov model, of high context order (typically 20). The method has been approached with a tool (also called SMASH). For visualization, SMASH outputs a SVG image, with an ideogram output architecture, where the patterns are represented with several HSV values (only value varies). The following image, illustrating the information maps between human and chimpanzee for the several chromosomes, depicts an example:

Address of the bookmark: https://github.com/pratas/smash

%MinMax: A versatile tool for calculating and comparing synonymous codon usage and its impact on protein folding.

Surabhi Chaudhary — Thu, 24 May 2018 02:53:31 -0500

%MM calculates whether a given gene sequence encodes amino acids using the most common codons possible, the least common codons possible, or (most typically) some combination of these extremes. See our PLoS ONE paper for more details on how the %MinMax algorithm works. %MinMax results are averaged over an 18-codon sliding window; hence the result for "codon window = 1" is the average codon usage for codons 1-18, codon window 2 = codons 2-19, etc.

Address of the bookmark: http://www.codons.org/

HiGlass: a tool for exploring genomic contact matrices and tracks.

Jit — Mon, 11 Jun 2018 09:44:49 -0500

HiGlass is a tool for exploring genomic contact matrices and tracks. Please take a look at the examples and documentation for a description of the ways that it can be configured to explore and compare contact matrices. To load private data, HiGlass can be run locally within a Docker container. The HiC data in the examples below is from Rao et al. (2014) http://higlass.io/

Address of the bookmark: http://higlass.io/

FMLRC: a long-read error correction tool using the multi-string Burrows Wheeler Transform

Neel — Fri, 10 Aug 2018 13:29:28 -0500

FMLRC, or FM-index Long Read Corrector, is a tool for performing hybrid correction of long read sequencing using the BWT and FM-index of short-read sequencing data. Given a BWT of the short-read sequencing data, FMLRC will build an FM-index and use that as an implicit de Bruijn graph. Each long read is then corrected independently by identifying low frequency k-mers in the long read and replacing them with the closest matching high frequency k-mers in the implicit de Bruijn graph. In contrast to other de Bruijn graph based implementations, FMLRC is not restricted to a particular k-mer size and instead uses a two pass method with both a short "k-mer" and a longer "K-mer". This allows FMLRC to correct through low complexity regions that are computational difficult for short k-mers.

Address of the bookmark: https://github.com/holtjma/fmlrc

ClipCrop: a tool for detecting structural variations with single-base resolution using soft-clipping information

Rahul Nayak — Thu, 04 Oct 2018 16:39:28 -0500

This is a tool for detecting structural variations using soft-clipping information From SAM files.

https://github.com/shinout/clipcrop

Address of the bookmark: https://github.com/shinout/clipcrop

Patterns: a modeling tool dedicated to biological network modeling

Abhimanyu Singh — Fri, 26 Jul 2019 01:11:59 -0500

It is designed to work with patterned data. Famous examples of problems related to patterned data are:

recovering signals in networks after a stimulation (cascade network reverse engineering),
analysing periodic signals.

Address of the bookmark: https://github.com/fbertran/Patterns

iSeqQC: a tool for expression-based quality control in RNA sequencing

BioStar — Sun, 16 Feb 2020 08:47:17 -0600

iSeqQC, an expression-based QC tool that detects outliers either produced due to variable laboratory conditions or due to dissimilarity within a phenotypic group. iSeqQC implements various statistical approaches including unsupervised clustering, agglomerative hierarchical clustering and correlation coefficients to provide insight into outliers.

http://cancerwebpa.jefferson.edu/iSeqQC/

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-3399-8

Address of the bookmark: https://github.com/gkumar09/iSeqQC

CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)

Jit — Mon, 18 May 2020 10:53:32 -0500

Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs. CAT and BAT can be run from intermediate steps if files are formated appropriately (see Usage).

Address of the bookmark: https://github.com/dutilh/CAT

vsFilt: A tool to improve virtual screening by structural filtration of docking poses

Neel — Wed, 25 Nov 2020 02:39:16 -0600

The vsFilt is the first open application for post-docking structural filtration, available as a web-server. The new tool is easy to use and configure to detect a wide range of interaction types that are known to be involved in molecular recognition, including hydrogen and halogen bonds, ionic interactions, hydrophobic contacts, π-stacking, and cation-π interactions. The web-server can process large libraries of up to 150’000 docked ligand poses. The results are web-based and can be operated on-line using the built-in HTML5 interactive analysis tools, or can be downloaded for a local use. The vsFilt is freely available on-line, no login required.

Address of the bookmark: https://biokinet.belozersky.msu.ru/vsfilt

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/