Abhimanyu Singh
A bioinformatics beginner
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Kaiju
By Jit 3050 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...CrocoBLAST: Optimized parallel implementation of local sequence alignment algorithms
By Jit 2657 days agowebchem.ncbr.muni.cz - Local sequence alignment is a cornerstone of bioinformatics, allowing to compare the amino-acid sequences of different proteins, or the nucleotide sequences of different pieces of DNA. The Basic Local Alignment Search Tool (BLAST) has revolutionized...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)...kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference...
By Jit 2520 days agosourceforge.net - Sept. 20, 2017 Version 3.1 released. Major upgrade. Version 3.1 fixes the problems with SNP annotation that arose when NCBI discontinued use of GI numbers. Please read carefully the Preface (page 3) and the File of annotated genomes section (pages...Scarpa
By Poonam Mahapatra 3034 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...MUMmer4: A fast and versatile genome alignment system
By Jit 2464 days agomummer4.github.io - MUMmer4, a substantially improved version of MUMmer that addresses genome size constraints by changing the 32-bit suffix tree data structure at the core of MUMmer to a 48-bit suffix array, and that offers improved speed through parallel processing...Aravind J Shankar gets all India rank 1 in BINC, 2016
By Jit 3028 days agoAravind J Shankar, a bioinformatics graduate of SASTRA University, has secured the all India rank 1 in BINCGenomeMapper: Simultaneous alignment of short reads against multiple genomes
By Jit 2353 days ago1001genomes.org - GenomeMapper is a short read mapping tool designed for accurate read alignments. It quickly aligns millions of reads either with ungapped or gapped alignments. It can be used to align against multiple genomes simulanteously or against a single...Find predicted CRISPR sites using Ensembl
By Jit 3020 days agoCas9 restricts DNA at specific Protospacer Adjacent Motifs (PAMs), which is species-dependent (for example, 5′ NGG 3′ for Streptococcus pyogenes Cas9).AlignQC: A tool for assessing an alignment, and generating reports that are easy to share
By Jit 2279 days agowww.healthcare.uiowa.edu - Long read alignment analysis. Generate a reports on sequence alignments for mappability vs read sizes, error patterns, annotations and rarefraction curve analysis. The most basic analysis only requires a BAM file, and outputs a web browser...
