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Results for "Genome"

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  • Poonam Mahapatra

    Gene Finding and Predictions

    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 signal, content and homology (protein and cDNA seq...

    Tags: Bioinformatics, Analysis, NGS, Gene, Prediction, Finding, Genome

    2859 days ago

  • Poonam Mahapatra

    Useful Bioinformatics Tools

    Collections of few handy tools for bioinformatician http://molbiol-tools.ca/Convert.htm

    Tags: Bioinformatics, Analysis, NGS, Tools, Gene, Genome, Format

    2856 days ago

  • Poonam Mahapatra

    Gaze for gene prediction http://www.ncbi.nlm.nih.gov/pmc/articles/PMC186661/ # Genes #Predictions #Genome #Tools #Gaze

    Tags: Predictions, Genome, Tools, Gaze

    2856 days ago

  • Poonam Mahapatra

    Ka, Ks and Ka/Ks calculations

    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 10 substitution rate estimation methods). gKaKs ...

    Tags: Bioinformatics, Analysis, NGS, Ka, Ks and Ka/Ks, calculations, Genome

    2856 days ago

  • Jitendra Narayan

    Comparative genomics resources https://www.dcode.org/ #Genomics #Resources #DCODE #Genome #Compare

    Tags: Genomics, Resources, DCODE, Genome, Compare

    2853 days ago

  • Jit

    Sushi: An R/Bioconductor package for visualizing genomic data

    Sushi: An R/Bioconductor package for visualizing genomic data

    Tags: Bioinformatics, Analysis, NGS, R, Plot, Sushi, Genome

    2854 days ago

  • Shruti Paniwala

    Artemis Comparison Tool (ACT)

    ACT is a Java application for displaying pairwise comparisons between two or more DNA sequences. It can be used to identify and analyse regions of similarity and difference between genomes and to explore conservation of synteny, in the context of the entire sequences and their annotation. It...

    Tags: Bioinformatics, Analysis, NGS, Artemis, Comparison Tool, ACT, Genome

    2847 days ago

  • Jit

    BRAKER: pipeline for fully automated prediction of protein coding genes with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes

    Gene finding in eukaryotic genomes is notoriously difficult to automate. The task is to design a work flow with a minimal set of tools that would reach state-of-the-art performance across a wide range of species. GeneMark-ET is a gene prediction tool that incorporates RNA-Seq data into unsupervis...

    Tags: Bioinformatics, Analysis, NGS, Braker, Annotation, Genes, Predictions, Genome

    2001 days ago

  • Jit

    Redundans

    Redundans pipeline assists an assembly of heterozygous genomes.Program takes as input assembled contigs, paired-end and/or mate pairs sequencing libraries and returns scaffolded homozygous genome assembly, that should be less fragmented and with total size ...

    Tags: Bioinformatics, Analysis, NGS, Redundans, Assembly, Heterozygous, Genome

    2853 days ago

  • Jit

    Plot genomoc data https://cran.r-project.org/web/packages/circlize/vignettes/genomic_plot.pdf #Circlize #R #Genome #Plot

    Tags: Circlize, R, Genome, Plot

    2853 days ago

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