Poonam Mahapatra
Bioinformatics Researcher
Latest comments
- Jit on Useful Bioinformatics Tools (2741 days ago): Collection of useful bioinformatics tools, specially for prokaryotes...
- Poonam Mahapatra on Velvet tutorial (2907 days ago): Velvet advicer http://dna.med.monash.edu.au/~torsten/velvet_advisor/
- Poonam Mahapatra on SAM flags (3069 days ago): Samtool WIKI http://davetang.org/wiki/tiki-index.php?page=SAMTools
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Bioinformatics, NGS, Analysis, Genome, Prediction, Gene, Assembly, Tools, Protein, sequence, DNA, SAM, Scaffolding, Velvet, Tutorial, Structure, program, Tool, regions, sequencing, Server, R, Data Mining, Easyfig, Fig, View, Flags, metagenomics, Oneliner, BAM, Visualization, Scarpa, WiseScaffolder, GeneValidator, Finding, Format, Ka, Ks and Ka/Ks, calculations, standardized-velvet-assembly-report, Guide, Project, Torrent, Mapping, TMAP, Tbl2asn, creation, records, submission, GenBank
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Poonam Mahapatra's bookmarks
Circlator: automated circularization of genome assemblies using long sequencing reads
By Poonam Mahapatra 2384 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...Protein Subcellular Localization Prediction
By Poonam Mahapatra 2459 days agoabi.inf.uni-tuebingen.de - Assigning subcellular localization to a protein is an important step towards elucidating its interaction partners, function, and potential role(s) in the cellular machinery. Computational tools offer an attractive complement to time-consuming and...JPred4: A Protein Secondary Structure Prediction Server
By Poonam Mahapatra 2521 days agowww.compbio.dundee.ac.uk - JPred4 (http://www.compbio.dundee.ac.uk/jpred4) is the latest version of the popular JPred protein secondary structure prediction server which provides predictions by the JNet algorithm, one of the most accurate methods for secondary structure...Tbl2asn: a command-line program that automates the creation of sequence records for submission to...
By Poonam Mahapatra 2735 days agowww.ncbi.nlm.nih.gov - Tbl2asn is a command-line program that automates the creation of sequence records for submission to GenBank. It uses many of the same functions as Sequin but is driven generally by data files. Tbl2asn generates .sqn files for submission to GenBank....TMAP - torrent mapping alignment program General Notes
By Poonam Mahapatra 2792 days agogithub.com - TMAP - torrent mapping alignment program General Notes TMAP is a fast and accurate alignment software for short and long nucleotide sequences produced by next-generation sequencing technologies. The latest TMAP is unsupported. To use a...Fools guide
By Poonam Mahapatra 2792 days agosfg.stanford.edu - This website and accompaning documents are intended as a tool to help researchers dealing with non-model organisms acquire and process transcriptomic high-throughput sequencing data without having to learn extensive bioinformatics skills. It covers...Velvet tutorial
By Poonam Mahapatra 2907 days ago Comments (1)evomics.org - The objective of this activity is to help you understand how to run Velvet in general, how to accurately estimate the insert size of a paired-end library through the use of Bowtie, the primary parameters of velvet, and the process...Standardized velvet assembly report
By Poonam Mahapatra 2907 days agogithub.com - Requirements: velvet (velveth velvetg should be in your PATH) R (with Sweave) pdflatex (usually part of TeTeX) ggplot2 (from R prompt type install.packages("ggplot2","proto","xtable")) Perl Optional: BLAT or BLAST (to generate...Ka, Ks and Ka/Ks calculations
By Poonam Mahapatra 3008 days agolonglab.uchicago.edu - gKaKs is a codon-based genome-level Ka/Ks computation pipeline developed and based on programs from four widely used packages: BLAT, BLASTALL (including bl2seq, formatdb and fastacmd), PAML (including codeml and yn00) and KaKs_Calculator (including...Useful Bioinformatics Tools
By Poonam Mahapatra 3009 days ago Comments (1)molbiol-tools.ca - Collections of few handy tools for bioinformatician http://molbiol-tools.ca/Convert.htm
