Rahul Nayak
A Bioinformatician
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MUMmer4: A fast and versatile genome alignment system
By Jit 2954 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...GenomeMapper: Simultaneous alignment of short reads against multiple genomes
By Jit 2843 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...Mulan: Multiple-sequence local alignment and visualization for studying function and evolution
By Jit 2752 days agowww.ncbi.nlm.nih.gov - Mulan: Multiple-sequence local alignment and visualization for studying function and evolution Mulan (http://mulan.dcode.org/), a novel method and a network server for comparing multiple draft and finished-quality sequences to identify functional...MSAProbs - Parallel and accurate multiple sequence alignment
By Neel 2432 days agomsaprobs.sourceforge.net - MSAProbs is a well-established state-of-the-art multiple sequence alignment algorithm for protein sequences. The design of MSAProbs is based on a combination of pair hidden Markov models and partition functions to calculate posterior...VG: variation graph data structures, interchange formats, alignment, genotyping, and variant...
By Jit 2230 days agogithub.com - Variation graphs provide a succinct encoding of the sequences of many genomes. A variation graph (in particular as implemented in vg) is composed of: nodes, which are labeled by sequences and ids edges, which connect two nodes via either of...UniAligner: a parameter-free framework for fast sequence alignment
By Abhi 728 days agogithub.com - UniAligner (formerly, TandemAligner) is the first parameter-free algorithm for sequence alignment that introduces a sequence-dependent alignment scoring that automatically changes for any pair of compared sequences. Classical alignment approaches,...Seal: SEquence ALignment evaluation suite
By Jit 2985 days agocompbio.case.edu - Seal is a comprehensive sequencing simulation and alignment tool evaluation suite. This software (implemented in Java) provides several utilities that can be used to evaluate alignment algorithms, including: Reading a pre-existing reference...Demo 4: Using BLAST/BLAT in Ensembl
By Radha Agarkar 4561 days agoWe demonstrate the BLAST/BLAT tool in Ensembl. Search for a sequence in Ensembl, and identify hits to the genome, or to genes, with this tool.Genome Workbench 2.10.7
By Gudiya Pal 3536 days agoGenome Workbench 2.10.7 is here! New features include added support for local custom BLAST databases and improvements to Tree View.BLAST+ 2.11.0 release is now available on FTP site !
By Jit 1938 days agoThe main advance is the ability to provide usage reports to NCBI to help us improve BLAST.
