The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here.
This edition of the Herald was brought to you by contribution from Istvan Albert, and was edited by Istvan Albert,
A unified VCF data set from nearly 1,500 diverse maize accessions and resources to explore the genomic landscape of maize | bioRxiv (www.biorxiv.org)
To address these continuity issues, The Maize Genetics and Genomics Database has collaborated with researchers in the maize community to offer variant data from a diverse set of 1,498 inbred lines, traditional varieties, and teosintes through a standardized variant-calling pipeline against version 5 of the B73 reference genome. The output was filtered for mapping quality, coverage, and linkage disequilibrium, and annotated based on variant effects relative to the B73 RefGen_v5 gene annotations.
submitted by: Istvan Albert
PhyKIT: A Multitool for Phylogenomics[v1] | Preprints.org (www.preprints.org)
PhyKIT is a tool for processing and analyzing the information content of multiple sequence alignments and phylogenetic trees. Here, we describe how to use PhyKIT for diverse analyses, including (i) constructing a phylogenomic supermatrix, (ii) detecting errors in orthology inference, (iii) quantifying biases in phylogenomic data sets, (iv) identifying radiation events or lack of resolution using gene support frequencies, and (v) conducting evolution-based screens to facilitate gene function prediction.
submitted by: Istvan Albert
Omics! Omics!: First Illumina Complete Long Reads Preprint (omicsomics.blogspot.com)
But now there is a preprint out on MedRxiv that reports iCLR results for a Genome In A Bottle (GIAB) sample as well as seven samples from individuals wiith potential genetic diseases of unresolved cause.
submitted by: Istvan Albert
Our deep learning strategy for analysing complex high-dimensional data--DeepMapper--is published. https://t.co/T2icwqp2tW
Short 🧵 pic.twitter.com/ZDyypGDmn2
— Martin Smith (@martinalexsmith) May 3, 2024
Our deep learning strategy for analysing complex high-dimensional data--DeepMapper--is published. https://t.co/T2icwqp2tW
Short 🧵 pic.twitter.com/ZDyypGDmn2
submitted by: Istvan Albert
Novel applications of Convolutional Neural Networks in the age of Transformers | Scientific Reports (www.nature.com)
Here we show that CNNs can recognise patterns in images with scattered pixels and can be used to analyse complex datasets by transforming them into pseudo images with minimal processing for any high dimensional dataset, representing a more general approach to the application of CNNs to datasets such as in molecular biology, text, and speech.
submitted by: Istvan Albert
VCF2PCACluster: a simple, fast and memory-efficient tool for principal component analysis of tens of millions of SNPs | BMC Bioinformatics | Full Text (bmcbioinformatics.biomedcentral.com)
We implemented five Kinship estimation methods and three clustering methods for its users to choose from. Moreover, unlike other PCA tools, VCF2PCACluster possesses a clustering function based on PCA result, which enabling users to automatically and clearly know about population structure. We demonstrated the same accuracy but a higher performance of this tool in performing PCA analysis on tens of millions of SNPs compared to another popular PLINK2 software, especially in peak memory usage that is independent of the number of SNPs in VCF2PCACluster.
submitted by: Istvan Albert
Just received my PhD diploma from ETH Zurich for opening the topic of A* for optimal sequence alignment.
My thesis argues that A* is natural for alignment by being heuristically fast and provably optimal. I feel lucky to poke such a fundamental problem yet I have no clue why… pic.twitter.com/bqKWnWGx13
— Pesho Ivanov 🇺🇦 (@peshotrie) May 2, 2024
Just received my PhD diploma from ETH Zurich for opening the topic of A* for optimal sequence alignment.
My thesis argues that A* is natural for alignment by being heuristically fast and provably optimal. I feel lucky to poke such a fundamental problem yet I have no clue why… pic.twitter.com/bqKWnWGx13
submitted by: Istvan Albert
The Genome Explorer Genome Browser | bioRxiv (www.biorxiv.org)
In this paper we report on a major update to our browser, Genome Explorer, that provides nearly instantaneous scaling and traversing of a genome, enabling users to quickly and easily zoom into an area of interest. The user can rapidly move between scales that depict the entire genome, individual genes, and the sequence; Genome Explorer presents the most relevant detail and context for each scale.
submitted by: Istvan Albert
Want to get the Biostar Herald in your email? Who wouldn't? Sign up righ'ere: toggle subscription
