Jit
Enthusiast computational biologist with business dream !!!
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Bienko and Crosetto Labs
We are two groups of scientists doing frontier research in quantitative biology and biomedicine. The Bienko group is interested in exploring the fundamental design principles controlling how DNA is packed in the eukaryotic nucleus and its relation...Magic-BLAST: a tool for mapping large next-generation RNA or DNA sequencing runs against a whole...
By Jit 3204 days agoncbi.github.io - Magic-BLAST is a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome. Each alignment optimizes a composite score, taking into account simultaneously the two reads of a pair, and in case of...ALPACA: A hybrid strategy for assembly of genomic DNA shotgun sequencing reads.
By Seema Singh 3080 days agogithub.com - ALPACA requires Celera Assembler 8.3 or later. It is recommended to build Celera Assembler from source. (Why? The pre-built binaries CA_8.3rc1 and CA8.3rc2 will work for any large data set. Detail paper...DeepVariant : an analysis pipeline that uses a deep neural network to call genetic variants from...
By Jit 2445 days agogithub.com - DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data. DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation...HNADOCK: a nucleic acid docking server for modeling RNA/DNA–RNA/DNA 3D complex structures
By Poonam Mahapatra 2313 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...The Ghost Ancestors Hidden in Our DNA
By Jitendra Narayan 48 days agoA fascinating new study published in Science (https://www.science.org/doi/10.1126/science.aef8874?) introduces a computational method called TRACE, which allows scientists to search modern human genomes for genetic traces of ancient populations that...LAST
By Archana Malhotra 3862 days agohttp://last.cbrc.jp/ - LAST can: Handle big sequence data, e.g: Compare two vertebrate genomes Align billions of DNA reads to a genome Indicate the reliability of each aligned column. Use sequence quality data properly. Compare DNA to proteins, with...gVolante: Completeness Assessment of Genome/Transcriptome Sequences
By Neel 2822 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...pbalign: maps PacBio reads to reference sequences and saves alignments to a BAM file
By Jit 3056 days agogithub.com - pbalign aligns PacBio reads to reference sequences, filters aligned reads according to user-specific filtering criteria, and converts the output to either the SAM format or PacBio Compare HDF5 (e.g., .cmp.h5) format. The output Compare HDF5 file...LTR_Finder: an efficient program for finding full-length LTR retrotranspsons in genome sequences.
By Neel 2822 days agogithub.com - LTR_Finder is an efficient program for finding full-length LTR retrotranspsons in genome sequences. The Program first constructs all exact match pairs by a suffix-array based algorithm and extends them to long highly similar pairs. Then...
