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 (2906 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
HNADOCK: a nucleic acid docking server for modeling RNA/DNA–RNA/DNA 3D complex structures
By Poonam Mahapatra 1632 days agohuanglab.phys.hust.edu.cn - The HNADOCK server is to predict the binding complex structure between two nucleic acid molecules through a hierarchical docking algorihtm of an FFT-based global search strategy and an intrinsic scoring function for nucleic acid interactions. Users...LRSDAY: Long-read Sequencing Data Analysis for Yeasts
By Poonam Mahapatra 1915 days agogithub.com - Long-read sequencing technologies have become increasingly popular in genome projects due to their strengths in resolving complex genomic regions. As a leading model organism with small genome size and great biotechnological importance, the budding...Miropeats: discovers regions of sequence similarity amongst any set of DNA sequences
By Poonam Mahapatra 1915 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...Many-to-many pairwise alignments of two sequence sets
By Poonam Mahapatra 2349 days agoemboss.sourceforge.net - needleall reads a set of input sequences and compares them all to one or more sequences, writing their optimal global sequence alignments to file. It uses the Needleman-Wunsch alignment algorithm to find the optimum alignment (including gaps) of two...“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files
By Poonam Mahapatra 2364 days agodoua.prabi.fr - One code to find them all is a set of perl scripts to extract useful information from RepeatMasker about transposable elements, retrieve their sequences and get some quantitative information. Assemble RepeatMasker hits into complete TE copies,...MCMCTREE: a phylogenetic program for Bayesian estimation of species divergence times
By Poonam Mahapatra 2366 days agowww.fish-evol.com - MCMCTREE is a phylogenetic program for Bayesian estimation of species divergence times using soft fossil constraints under various molecular clock models. This is part of the PAML package. In this tutorial I will analyze an easy...GLEAN: an unsupervised learning system to integrate disparate sources of gene structure evidence
By Poonam Mahapatra 2366 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...Gblocks: eliminates poorly aligned positions and divergent regions of a DNA or protein alignment
By Poonam Mahapatra 2366 days agomolevol.cmima.csic.es - Gblocks eliminates poorly aligned positions and divergent regions of a DNA or protein alignment so that it becomes more suitable for phylogenetic analysis. This server implements the most important features of the Gblocks program to make its...SOAP2 : Short Oligonucleotide Analysis Package 2
By Poonam Mahapatra 2376 days agosoap.genomics.org.cn - SOAPaligner/soap2 is a member of the SOAP (Short Oligonucleotide Analysis Package). It is an updated version of SOAP software for short oligonucleotide alignment. The new program features in super fast and accurate alignment for huge amounts of...TACOA: Taxonomic classification of environmental genomic fragments using a kernelized nearest...
By Poonam Mahapatra 2384 days agowww.cebitec.uni-bielefeld.de - TACOA is a software that can accurately predict the taxonomic origin of genomic fragments from metagenomic data sets by combining the advantages of the k -NN approach with a smoothing kernel function. TACOA can be easily installed and run on a...
