Archana Malhotra
Computational Biologist
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Is reference genome necessary for gene expression study in transcriptome sequencing or for variant...
Started by Rahul Agarwal 4195 days agoLike in case of plant genomes where nature of genome is too complex and huge in size to accomplish complete de novo assembly by current sequencing technology. What would be alternate solution? Can we live in reference free world?Scripted DNA !!!
By Jit 3434 days agoAs per bioinformatician DNA is partially scripted ;) You dont believe in it. Please have a look at image carefully:)Managing and Analyzing Next-Generation Sequence Data
By Rahul Agarwal 3898 days agowww.ploscompbiol.org - Centralized Bioinformatics Core Facilities provide shared resources for the computational and IT requirements of the investigators in their department or institution. As such, they must be able to effectively react to new types of experimental...Miropeats: discovers regions of sequence similarity amongst any set of DNA sequences
By Poonam Mahapatra 1964 days agowww.littlest.co.uk - Miropeats discovers regions of sequence similarity amongst any set of DNA sequences and then presents this similarity information graphically. Sequence similarity searching is a very general tool that forms the basis of many different biological...List of motif discovery tools !
By Neel 2243 days ago Comments (2)A DNA sequence motif represented as a sequence logo for the LexA-binding motif. IThe 8000 years old Tibetian gene mutation !!!
By Neel 3796 days agoA study led by University of Utah scientists is the first to find a genetic cause for the adaptation, a single DNA base pair change that dates back 8,000 years and demonstrate how it contributes to the Tibetans' ability to live in low oxygen...COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly
By Jit 2592 days agoftp.genomics.org.cn - An efficient tool called Connecting Overlapped Pair-End (COPE) reads, to connect overlapping pair-end reads using k-mer frequencies. We evaluated our tool on 30× simulated pair-end reads from Arabidopsis thaliana with 1% base error. COPE...
Tools for bacterial whole genome annotation
Last updated 2582 days ago by Radha AgarkarRAST – Web tool (upload contigs), uses the subsystems in the SEED database and provides detailed annotation and pathway analysis. Takes several hours per genome but I think this is the best way to get a high quality annotation...Circlator: automated circularization of genome assemblies using long sequencing reads
By Poonam Mahapatra 2432 days agosanger-pathogens.github.io - A tool to circularize genome assemblies. The algorithm and benchmarks are described in the Genome Biology manuscript. Citation: "Circlator: automated circularization of genome assemblies using long sequencing reads", Hunt et al, Genome Biology...Roderic Guigó Lab
Research in our group focuses on the investigation of the signals involved in gene specification in genomic sequences (promoter elements, splice sites, translation initiation sites, etc…). We are interested both in the mechanism of their recognition...
