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DAGchainer: Computing Chains of Syntenic Genes in Complete Genomes
By Abhimanyu Singh 2815 days agodagchainer.sourceforge.net - The DAGchainer software computes chains of syntenic genes found within complete genome sequences. As input, DAGchainer accepts a list of gene pairs with sequence homology along with their genome coordinates. Using a scoring function which accounts...ConPADE: Genome Assembly Ploidy Estimation from Next-Generation Sequencing Data
By Jit 2808 days agogithub.com - ConPADE (Contig Ploidy and Allele Dosage Estimation), a probabilistic method that estimates the ploidy of any given contig/scaffold based on its allele proportions. In the process, they report findings regarding errors in sequencing. The method can...PBSuite: Software for Long-Read Sequencing Data from PacBio
By Jit 2805 days agosourceforge.net - PBJelly - the genome upgrading tool. PBHoney - the structural variation discovery tool Both are contained within the PBSuite code found in downloads.----- PBJelly -----Read The...MyCC: Accurate binning of metagenomic contigs via automated clustering sequences using information...
By Jit 2801 days agosourceforge.net - MyCC, an automated binning tool that combines genomic signatures, marker genes and optional contig coverages within one or multiple samples, in order to visualize the metagenomes and to identify the reconstructed genomic fragments. More...Prokka: tool for the rapid annotation of prokaryotic genomes
By Jit 2798 days agowww.vicbioinformatics.com - Prokka is a software tool for the rapid annotation of prokaryotic genomes. A typical 4 Mbp genome can be fully annotated in less than 10 minutes on a quad-core computer, and scales well to 32 core SMP systems. It produces GFF3, GBK and SQN files...COCACOLA (binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment, and...
By Jit 2797 days agogithub.com - COCACOLA is a general framework that combines different types of information: sequence COmposition, CoverAge across multiple samples, CO-alignment to reference genomes and paired-end reads LinkAge to automatically bin contigs into OTUs. Furthermore,...Selecting between Python 2 and Python 3?
Started by Rahul Agarwal 4133 days ago Replies (1) Last reply by Jitendra Narayan 4133 days agoWhich version is best for bioinformatician to work on?sequenceserver
By Jit 2794 days agogithub.com - SequenceServer lets you rapidly set up a BLAST+ server with an intuitive user interface for use locally or over the web. More at http://sequenceserver.com.Research Fellow
UNIVERSITY OF CALCUTTA A walk-in-interview will be held on 15.7.2013 at 12 noon in the Department of Biophysics, Molecular Biology and Bioinformatics, 92 A.P.C Road, Kolkata-700 009 to select one trainee research fellow and two students under...Dumontier Lab
Our research aims to better understand how living systems respond to chemical agents. A key aspect of our approach involves using computational frameworks that are powered by formal (i.e. machine understandable) semantics to make effectively use of...
