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gVolante: Completeness Assessment of Genome/Transcriptome Sequences
By Neel 2141 days agogvolante.riken.jp - A brand-new web server, gVolante, which provides an online tool for (i) on-demand completeness assessment of sequence sets by means of the previously developed pipelines CEGMA and BUSCO and (ii) browsing pre-computed completeness scores for publicly...Nucl2Vec: Local alignment of DNA sequences using Distributed Vector Representation
By Jit 1348 days agoprakharg24.github.io - We demonstrate a novel approach forlocal alignment of DNA reads with respect to reference genome.For this process we have used Skip-gram model for creatingencoding(Nucl2Vec) and k-nearest neighbor for the alignment.With our new approach we have...minimap2: A versatile pairwise aligner for genomic and spliced nucleotide sequences
By Jit 2348 days agogithub.com - git clone https://github.com/lh3/minimap2 cd minimap2 && make # long sequences against a reference genome ./minimap2 -a test/MT-human.fa test/MT-orang.fa > test.sam # create an index first and then map ./minimap2 -d MT-human.mmi...RopeBWT2: Incremental construction of FM-index for DNA sequences
By Rahul Nayak 2221 days agogithub.com - RopeBWT2 is an tool for constructing the FM-index for a collection of DNA sequences. It works by incrementally inserting one or multiple sequences into an existing pseudo-BWT position by position, starting from the end of the sequences. This...FGENESH - Program for predicting multiple genes in genomic DNA sequences
By BioStar 2165 days agowww.softberry.com - FGENESH is the fastest (50-100 times faster than GenScan) and most accurate gene finder available - see the figure and the table below. In recent rice genome sequencing projects, it was cited "the most successful (gene finding) program (Yu et...Gepard: allows the calculation of dotplots even for large sequences like chromosomes or bacterial...
By Jit 1916 days agogithub.com - Gepard (German: "cheetah", Backronym for "GEnome PAir - Rapid Dotter") allows the calculation of dotplots even for large sequences like chromosomes or bacterial genomes. Reference: Krumsiek J, Arnold R, Rattei T. Gepard: A rapid and sensitive tool...Sequence Tube Maps: displays multiple genomic sequences in the form of a tube map
By Jit 1719 days agogithub.com - A JavaScript module for the visualization of genomic sequence graphs. It automatically generates a "tube map"-like visualization of sequence graphs which have been created with vg. (https://github.com/vgteam/vg) Link to working demo:...kebabs: package provides functionality for kernel based analysis of biological sequences via...
By Rahul Nayak 996 days agowww.bioinf.jku.at - 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...doubletrouble: identify duplicated genes from whole-genome protein sequences and classify
By LEGE 263 days agobioconductor.org - 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...EMBL Postdoc position in Bacterial Gene Gain Loss
A post-doctoral fellowship is available in the research groups of Nick Goldman (EBI) and John Welch (Genetics Department, Cambridge University) under the EMBL-EBI / Cambridge Computational Biomedical Postdoctoral Fellowship scheme. The project is...
