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
Tag cloud
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
Gene Finding and Predictions
By Poonam Mahapatra 3011 days agogenome.crg.es - In this exercise, a previously annotated gene will be used to measure the accuracy of different gene finding approaches. GRAIL, GENSCAN, geneid, FGENESH, GenomeScan, GrailEXP and GENEWISE will be used to annotate the sequence. Both search by...GeneValidator - Identify problems with predicted genes
By Poonam Mahapatra 3011 days agogithub.com - GeneValidator helps in identifing problems with gene predictions and provide useful information extracted from analysing orthologs in BLAST databases. The results produced can be used by biocurators and researchers who need accurate gene...WiseScaffolder
By Poonam Mahapatra 3055 days agoabims.sb-roscoff.fr - Function WiseScaffolder is a stand-alone semi-automatic application for genome scaffolding of pre-assembled contigs using mate-pair data. It also produces editable scaffold maps, allowing either to build gapped scaffolds or usable as a common...Scarpa
By Poonam Mahapatra 3055 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...Fancy Oneliner for Bioinformatics !!
By Poonam Mahapatra 3061 days agouserweb.eng.gla.ac.uk - This webpage lists some of the one-liners that we frequently use in metagenomic analyses. You can click on the following links to browse through different topics. You can copy/paste the commands as they are in your terminal screen, provided you...SAM flags
By Poonam Mahapatra 3069 days ago Comments (4)broadinstitute.github.io - Decoding SAM flags This utility makes it easy to identify what are the properties of a read based on its SAM flag value, or conversely, to find what the SAM Flag value would be for a given combination of properties. To decode a given SAM flag...Easyfig
By Poonam Mahapatra 3130 days agoeasyfig.sourceforge.net - Easyfig has moved to github, for newer releases of Easyfig please visit our new webpage - https://mjsull.github.io/Easyfig. Easyfig is a Python application for creating linear comparison figures of multiple genomic loci with an easy-to-use...Bioinformatics software for biologists in the genomics era
By Poonam Mahapatra 3989 days ago Comments (1)bioinformatics.oxfordjournals.org - The genome sequencing revolution is approaching a landmark figure of 1000 completely sequenced genomes. Coupled with fast-declining, per-base sequencing costs, this influx of DNA sequence data has encouraged laboratory scientists to engage large...Rdatamining.com : R and Data Mining
By Poonam Mahapatra 4118 days agowww.rdatamining.com - This website presents examples, documents and resources on data mining with R. Documents on using R for data mining are available to download for non-commercial personal use, including R Reference card for Data Mining, R and Data Mining:...
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