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S-plot2: Rapid Visual and Statistical Analysis of Genomic Sequences
By Abhimanyu Singh 2255 days agobitbucket.org - S-plot2 creates an interactive, two-dimensional heatmap capturing the similarities and dissimilarities in nucleotide usage between genomic sequences (partial or complete). In S-plot2, whole eukaryotic chromosomes and smaller prokaryotic genomes can...Predict Gene Ontology with sequences !
By LEGE 1610 days agoekhidna2.biocenter.helsinki.fi - PANNZER (Protein ANNotation with Z-scoRE) is a fully automated service for functional annotation of prokaryotic and eukaryotic proteins of unknown function. The tool is designed to predict the functional description (DE) and GO...minimap2: A versatile pairwise aligner for genomic and spliced nucleotide sequences
By Jit 2359 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...COSINE: non-seeding method for mapping long noisy sequences
By Jit 2232 days agogithub.com - Third generation sequencing (TGS) are highly promising technologies but the long and noisy reads from TGS are difficult to align using existing algorithms. Here, we present COSINE, a conceptually new method designed specifically for aligning long...UPhO: Scripts for homology and orthology assessment from genomic sequences.
By BioStar 2151 days agogithub.com - UPhO finds orthologs with and without inparalogs from input gene family trees. Refer to the Documentation.pdf for more detailed explanations on its usage, installation and dependencies. Type UPhO.py -h for help. The only input requierement for UPhO...Curated set of ribosomal RNA (rRNA) reference sequences (targeted loci) with verifiable organism
By Rahul Nayak 1746 days agoMCBI have a curated set of ribosomal RNA (rRNA) reference sequences (targeted loci) with verifiable organism sources and current names. This set is critical for correctly identifying and classifying prokaryotic (bacteria and archaea) and fungal...Tiara: deep learning-based classification system for eukaryotic sequences
By Rahul Nayak 996 days agoacademic.oup.com - With a large number of metagenomic datasets becoming available, eukaryotic metagenomics emerged as a new challenge. The proper classification of eukaryotic nuclear and organellar genomes is an essential step toward a better understanding of...Genome Annotation
By Manshi Raghubanshi 4119 days agoDr. Rob Edwards describes some of the problems, challenges, and approches in genome annotation, with a particular emphasis on how the Fellowship for the Interpretation of Genomes (FIG) developed subsystems using the SEED database available at...BUSCO
By Jitendra Narayan 3223 days agohttp://busco.ezlab.org/ - Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs More at http://busco.ezlab.org/
