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Maq: Mapping and Assembly with Quality
By Jit 3545 days agomaq.sourceforge.net - Maq stands for Mapping and Assembly with Quality It builds assembly by mapping short reads to reference sequences. Maq is a project hosted by SourceForge.net. The project page is available athttp://sourceforge.net/projects/maq/....eQuant : energy-based quality assessment of protein
By Shruti Paniwala 3330 days agobiosciences.hs-mittweida.de - Protein structures are of varying quality. Especially, in-silico modeled structures are prone to contain serious errors, which limit the usefulness and reliability of these particular protein structures.eQuant is a service for structure...Merqury: reference-free quality and phasing assessment for genome assemblies
By Jit 2253 days agogithub.com - Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual. The k-mer spectrum of this read set can be used for independently evaluating assembly quality without the need of a high quality...RNA Sequencing Helps Identify Functional Variants from GWAS
By Andaleeb 4640 days agoschizophreniaforum.org - For Alzheimer’s and other complex disorders, mining the genome for disease-associated variants is no longer the obstacle. The challenge nowadays is figuring out how the identified loci relate to disease. As reported last month in Nature and...Hoffman Lab
They develop machine learning techniques to better understand chromatin biology. These models and algorithms transform high-dimensional functional genomics data into interpretable patterns and lead to new biological...Barrnap: Bacterial ribosomal RNA predictor
By Abhimanyu Singh 3373 days agogithub.com - Barrnap predicts the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S). It takes FASTA DNA sequence as input, and write GFF3 as output....HNADOCK: a nucleic acid docking server for modeling RNA/DNA–RNA/DNA 3D complex structures
By Poonam Mahapatra 2254 days agohuanglab.phys.hust.edu.cn - The HNADOCK server is to predict the binding complex structure between two nucleic acid molecules through a hierarchical docking algorihtm of an FFT-based global search strategy and an intrinsic scoring function for nucleic acid interactions. Users...Tools for RNA classification
By Abhi 1368 days ago Comments (1)The method used to isolate, enrich and sequence a sample will affect the composition of the sequencing data in terms of the types of RNA species represented and their relative abundancesUnderstanding RNA-Seq Normalization Methods: TPM vs. FPKM vs. CPM
By Neel 604 days agoChoosing the right normalization method depends on the specific objectives of your RNA-Seq analysis. TPM’s proportionality and robustness make it the preferred choice for most applications, while CPM serves well for differential expression...
