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Tools

Tools are in free access Public access or restricted access Registered access

They run on the web, unix or both.

Tools in restricted access can use unpublished data.


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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 ...

Tedna is a lightweight de novo transposable element assembler. It assembles the transposable elements directly from the raw reads.Last version: 1.2.2
  • Source code: 
  • Binary: 
  • Changes:
    • Removed autotools. It never like me.
    • Added a "version" parameter in command ...

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