Rahul Nayak
A Bioinformatician
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GLEAN: an unsupervised learning system to integrate disparate sources of gene structure evidence
By Poonam Mahapatra 2973 days agosourceforge.net - GLEAN is an unsupervised learning system to integrate disparate sources of gene structure evidence (gene model predictions, EST/protein genomic sequence alignments, SAGE/peptide tags, etc) to produce a consensus gene prediction, without prior...HGTector: an automated method facilitating genome-wide discovery of putative horizontal gene...
By Jit 2740 days agogithub.com - A computational pipeline for genome-wide detection of putative horizontal gene transfer (HGT) events based on sequence homology search hit distribution statistics Authors: Qiyun Zhu (qiyunzhu@gmail.com), Katharina Dittmar...MAGIC: A tool for predicting transcription factors and cofactors driving gene sets using ENCODE data
By BioStar 2064 days agogithub.com - The algorithm presented herein, Mining Algorithm for GenetIc Controllers (MAGIC), uses ENCODE ChIP-seq data to look for statistical enrichment of TFs and cofactors in gene bodies and flanking regions in gene lists without...OMArk: software for proteome (protein-coding gene repertoire) quality assessment
By LEGE 882 days agogithub.com - OMArk is a software for proteome (protein-coding gene repertoire) quality assessment. It provides measures of proteome completeness, characterizes the consistency of all protein coding genes with regard to their homologs, and identifies the presence...Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads
By Rahul Nayak 2834 days agosourceforge.net - Rainbow is developed to provide an ultra-fast and memory-efficient solution to clustering and assembling short reads produced by RAD-seq. First, Rainbow clusters reads using a spaced seed method. Then, Rainbow implements a heterozygote calling like...MetaPred2CS
By Manisha Mishra 3429 days agogithub.com - MetaPred2CS Web server is a meta-predictor based on Support Vector Machine (SVM) that combines 6 individual sequence based protein-protein interaction prediction methods to predict prokaryotic two-component...Anvio
By Shruti Paniwala 3688 days agogithub.com - In a nutshell Anvi’o is an analysis and visualization platform for ‘omics data. Please find the methods paper here: https://peerj.com/articles/1319/ Anvi’o would not have been possible without the help of many people who...Genome Workbench 2.10.7
By Gudiya Pal 3673 days agoGenome Workbench 2.10.7 is here! New features include added support for local custom BLAST databases and improvements to Tree View.Scarpa
By Poonam Mahapatra 3662 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...VAGUE:Velvet Assembler Graphical Front End
By Jit 3436 days agowww.vicbioinformatics.com - VAGUE is a vague acronym for "Velvet Assembler Graphical Front End", which means it is a GUI for the Velvet de novo assembler. The command line version of Velvet can be complicated for beginners to use, but VAGUE makes it clear and simple More...
