Results for "Analysis"


  • TEannot

    We advise to run first the TEdenovo pipeline but it is not compulsory. We suppose you begin by running the TEannot pipeline on the example provided in the directory "db/" rather than directly on your own genomic sequences. Thus, from now on, the project name is "DmelChr4".  

    Tags: Bioinformatics, Analysis, NGS, TEs, TEannot, REPET, Pipeline, Repeats, Genome

    339 days ago

  • vcfR

    Most variant calling pipelines result in files containing large quantities of variant information. The variant call format (vcf) is an increasingly popular format for this data. The format of these files and their content is discussed in the vignette ‘vcf data.’ These files ...

    Tags: Bioinformatics, Analysis, NGS, vcfR, R, Visualization, VCF, Genome

    338 days ago

  • GeneMANIA

    Faster, more accurate algorithms function prediction "GeneMANIA (Multiple Association Network Integration Algorithm)" have however been developed in recent years and are publicly available on the web, indicating the future direction of function prediction.

    Tags: Bioinformatics, Analysis, NGS, Annotation, Genome

    335 days ago

  • TGNet

    Recent technological progress has greatly facilitated de novo genome sequencing. However, de novo assemblies consist in many pieces of contiguous sequence (contigs) arranged in thousands of scaffolds instead of small numbers of chromosomes. Confirming and improving the quality...

    Tags: Bioinformatics, Analysis, NGS, Stats, Assemble, Plot, TGNet, Visualize, Genome

    333 days ago


    A probabilistic framework for structural variant discovery. Ryan M Layer, Colby Chiang, Aaron R Quinlan, and Ira M Hall. 2014. "LUMPY: a Probabilistic Framework for Structural Variant Discovery." Genome Biology 15 (6): R84. doi:10.1186/gb-2014-15-6-r84. More at

    Tags: Bioinformatics, Analysis, NGS, Lumpy, SV, Variation, Structure, Genome

    332 days ago

  • GeneValidator - Identify problems with predicted genes

    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 predictions. If you would like to use GeneValidator on a f...

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

    331 days ago

  • 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

    331 days ago

  • Useful Bioinformatics Tools

    Collections of few handy tools for bioinformatician

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

    328 days ago

  • 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

    328 days ago

  • 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

    326 days ago