<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/44364?offset=50 https://bioinformaticsonline.com/bookmarks/view/43815/kebabs-package-provides-functionality-for-kernel-based-analysis-of-biological-sequences-via-support-vector-machine-svm-based-methods Fri, 04 Mar 2022 00:14:11 -0600 https://bioinformaticsonline.com/bookmarks/view/43815/kebabs-package-provides-functionality-for-kernel-based-analysis-of-biological-sequences-via-support-vector-machine-svm-based-methods <![CDATA[kebabs: package provides functionality for kernel based analysis of biological sequences via Support Vector Machine (SVM) based methods]]> The kebabs package provides functionality for kernel based analysis of biological sequences via Support Vector Machine (SVM) based methods. Biological sequences include DNA, RNA, and amino acid (AA) sequences. Sequence kernels define similarity measures between sequences. The package implements some of the most important kernels for sequence analysis in a very flexible and efficient way and extends the standard position-independent functionality of these kernels in a novel way to take the position of patterns in the sequences into account for the similarity measure.

http://www.bioinf.jku.at/software/kebabs/

http://bioconductor.org/packages/release/bioc/vignettes/kebabs/inst/doc/kebabs.pdf

Address of the bookmark: http://www.bioinf.jku.at/software/kebabs/

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/44479/doubletrouble-identify-duplicated-genes-from-whole-genome-protein-sequences-and-classify Tue, 05 Mar 2024 00:23:49 -0600 https://bioinformaticsonline.com/bookmarks/view/44479/doubletrouble-identify-duplicated-genes-from-whole-genome-protein-sequences-and-classify <![CDATA[doubletrouble: identify duplicated genes from whole-genome protein sequences and classify]]> doubletrouble aims to identify duplicated genes from whole-genome protein sequences and classify them based on their modes of duplication. The duplication modes are i. segmental duplication (SD); ii. tandem duplication (TD); iii. proximal duplication (PD); iv. transposed duplication (TRD) and; v. dispersed duplication (DD). Transposon-derived duplicates (TRD) can be further subdivided into rTRD (retrotransposon-derived duplication) and dTRD (DNA transposon-derived duplication). If users want a simpler classification scheme, duplicates can also be classified into SD- and SSD-derived (small-scale duplication) gene pairs. Besides classifying gene pairs, users can also classify genes, so that each gene is assigned a unique mode of duplication. Users can also calculate substitution rates per substitution site (i.e., Ka and Ks) from duplicate pairs, find peaks in Ks distributions with Gaussian Mixture Models (GMMs), and classify gene pairs into age groups based on Ks peaks.

Address of the bookmark: https://bioconductor.org/packages/release/bioc/html/doubletrouble.html

]]> LEGE https://bioinformaticsonline.com/bookmarks/view/44896/jaeger-an-accurate-and-fast-deep-learning-tool-to-detect-bacteriophage-sequences Sun, 31 Aug 2025 06:30:16 -0500 https://bioinformaticsonline.com/bookmarks/view/44896/jaeger-an-accurate-and-fast-deep-learning-tool-to-detect-bacteriophage-sequences <![CDATA[Jaeger : an accurate and fast deep-learning tool to detect bacteriophage sequences]]> Jaeger is a tool that utilizes homology-free machine learning to identify phage genome sequences that are hidden within metagenomes. It is capable of detecting both phages and prophages within metagenomic assemblies.

Address of the bookmark: https://github.com/MGXlab/Jaeger

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