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Tools in restricted access can use unpublished data.


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The TE_finder suite gathers C++ programs developed for transposable element search and their annotation in large eukaryotic genome sequence. But we think that the tools are generic enough to be used in other contexts.The suite is mainly composed by four programs BLASTER, MATCHER, GROUPER, ...

Prediction of transmembrane helices in proteins.
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Locate and display tandem repeats in DNA sequences.
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Tablet is a lightweight, high-performance graphical viewer for next generation sequence assemblies and alignments.
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TargetP 1.1 predicts the subcellular location of eukaryotic proteins. The location assignment is based on the predicted presence of any of the N-terminal presequences: chloroplast transit peptide (cTP), mitochondrial targeting peptide (mTP) or secretory pathway signal peptide (SP). For the sequences predicted ...

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Tedna is a lightweight de novo transposable element assembler. It assembles the transposable elements directly from the raw reads.Last version: 1.3
  • Source code in github
  • Changes: Long reads as input are available.
Previous versions
  • Version 1.2.2
    • Source code: ...

A fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.More information is available on TopHat Web ...

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Trans-ABySS is a software pipeline for analyzing ABySS-assembled contigs from shotgun transcriptome data.The pipeline accepts assemblies that were generated across a wide range of k values in order to address variable transcript expression levels. It first filters and merges the multi-k assemblies, generating a ...

Computational structural and functional analysis of plant genomic sequences (BAC/Contigs/Scaffolds/Pseudomolecules)TriAnnot web pages
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Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line.The current trimming steps are:
  • ILLUMINACLIP: Cut adapter and other illumina-specific sequences from the read.

Probably the most widely tool to search for tRNA genes in genomic sequence.A Web server is available at Lowe lab.
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Update: 02 Dec 2011
Creation date: 31 May 2011
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