Abhimanyu Singh
A bioinformatics beginner
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EuGI: a novel resource for studying genomic islands to facilitate horizontal gene transfer...
By Surabhi Chaudhary 2417 days agobmcgenomics.biomedcentral.com - SWGIS v2.0 along with the EuGI database, which houses GIs identified in 66 different eukaryotic species, and the EuGI web-resource, provide the first comprehensive resource for studying HGT in...ShadowCaster: a hybrid approach for the detection of horizontal gene transfer events in prokaryotes
By Jit 1623 days agogithub.com - ShadowCaster implements an evolutionary model to calculate Bayesian likelihoods for each ‘alien genes’ with an unusual sequence composition according to the host genome background to detect HGT events in...DarkHorse: a method for genome-wide prediction of horizontal gene transfer
By Jit 2741 days agowww.ncbi.nlm.nih.gov - A new approach to rapid, genome-wide identification and ranking of horizontal transfer candidate proteins is presented. The method is quantitative, reproducible, and computationally undemanding. It can be combined with genomic signature and/or...GWASpro: A High-Performance Genome-Wide Association Analysis Server
By Rahul Nayak 2208 days agobioinfo.noble.org - GWASpro supports building complex design matrices, by which complex experimental designs that may include replications, treatments, locations and times, can be accounted for in the linear mixed model (LMM). GWASpro is optimized to handle GWAS data...Mulan: MUltiple sequence Local AligNment and conservation visualization tool
By Rahul Nayak 2713 days agomulan.dcode.org - Mulan performs multiple (2 or more) sequence alignments with an efficient and rapid "full local" alignment strategy that ensures a recapitulation of evolutionary sequence rearrangements (such as inversions and reshuffling) in any of the species. It...CrocoBLAST: Optimized parallel implementation of local sequence alignment algorithms
By Jit 2708 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...GSP4PDB: a web tool to visualize, search and explore protein-ligand structural patterns
By Neel 1744 days agogdblab.com - GSP4PDB is a user-friendly and efficient application to search and discover new patterns of protein-ligand interaction. GSP4PDB is part of the services provided by the Bioinformatic Group of the University of...Syri compares alignments between two chromosome-level assemblies and identifies synteny and...
By Shruti Paniwala 936 days agogithub.com - Syri compares alignments between two chromosome-level assemblies and identifies synteny and structural rearrangements.Minda: a tool for evaluating structural variant (SV) callers
By LEGE 267 days agogithub.com - Minda is a tool for evaluating structural variant (SV) callers that standardizes VCF records for compatibility with both germline and somatic SV callers, benchmarks against a single VCF input file, or benchmarks against an ensemble call set...
