Abhimanyu Singh
A bioinformatics beginner
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Nucl2Vec: Local alignment of DNA sequences using Distributed Vector Representation
By Jit 1819 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...Kaiju
By Jit 3542 days agohttp://kaiju.binf.ku.dk/ - Kaiju is a program for the taxonomic classification of metagenomic high-throughput sequencing reads. Each read is directly assigned to a taxon within the NCBI taxonomy by comparing it to a reference database containing microbial and viral protein...Harvest: a suite of core-genome alignment and visualization tools
By Jit 3013 days agoharvest.readthedocs.io - Harvest is a suite of core-genome alignment and visualization tools for quickly analyzing thousands of intraspecific microbial genomes, including variant calls, recombination detection, and phylogenetic trees. Tools Parsnp - Core-genome...Bioinformatics openings at ICGEB NEW DELHI, INDIA
Applications are invited for: ICGEB NEW DELHI, INDIA Biotechnology research positions Projects include: a) protein structure determination b) malaria parasite biology c) genomics and metagenomics d) molecular and cellular biology e)...xmatchview: smith-waterman alignment visualization
By Rahul Nayak 2993 days agogithub.com - xmatchview and xmatchview-conifer are imaging tools for comparing the synteny between DNA sequences. It allows users to align 2 DNA sequences in fasta format using cross_match and displays the alignment in a variety of image formats. xmatchview and...Scarpa
By Poonam Mahapatra 3526 days agocompbio.cs.toronto.edu - Scarpa is a stand-alone scaffolding tool for NGS data. It can be used together with virtually any genome assembler and any NGS read mapper that supports SAM format. Other features include support for multiple libraries and an option to estimate...minialign: fast and accurate alignment tool for PacBio and Nanopore long reads
By Jit 2846 days agogithub.com - Minialign is a little bit fast and moderately accurate nucleotide sequence alignment tool designed for PacBio and Nanopore long reads. It is built on three key algorithms, minimizer-based index of the minimap overlapper, array-based seed chaining,...Aravind J Shankar gets all India rank 1 in BINC, 2016
By Jit 3520 days agoAravind J Shankar, a bioinformatics graduate of SASTRA University, has secured the all India rank 1 in BINC
Understanding BLASTn output format 6 !
Last updated 2812 days ago by Rahul NayakBLASTn output format 6 BLASTn maps DNA against DNA, for example gene sequences against a reference genomeblastn -query genes.ffn -subject genome.fna -outfmt 6 BLASTn tabular output format 6 Column headers:qseqid sseqid pident...Find predicted CRISPR sites using Ensembl
By Jit 3512 days agoCas9 restricts DNA at specific Protospacer Adjacent Motifs (PAMs), which is species-dependent (for example, 5′ NGG 3′ for Streptococcus pyogenes Cas9).
