Tn-seq Explorer 1.5B – Analysis of High-throughput Sequencing data of Transposon Mutant Libraries

TARGeT (Tree Analysis of Related Genes and Transposons) uses either a DNA or amino acid ‘seed’ query to: (i) automatically identify and retrieve gene family homologs from a genomic database, (ii) characterize gene structure and (iii) perform phylogenetic analysis. Due to its high speed, TARGeT is also able to characterize very large gene families, including transposable elements (TEs).

::DEVELOPER

TARGet team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Yujun Han, James M. Burnette III and Susan R. Wessler
TARGeT: a web-based pipeline for retrieving and characterizing gene and transposable element families from genomic sequences
Nucl. Acids Res. (2009) 37 (11): e78.

MH-ESS 1.21 – Bayesian Analysis of Transposon Mutagenesis Data

MH-ESS 1.21

:: DESCRIPTION

MH-ESS is a python implementation of the Bayesian analysis method. It utilizes read information obtained from sequencing libraries of transposon mutants, to determine the essentiality of genes. Using a Bayesian framework, essentiality is modeled through the Extreme Value (Gumbel) distribution, which characterizes the maximum run of non-insertions (i.e. number of consecutive TA sites lacking insertion in a row). Genes with significantly larger runs of non-insertion thant statistically expected have a higher likelihood of essentiality. A Metropolis-Hastings sampling procedure is utilized to sample from conditional densities of essentiality for all genes, and posterior estimates of the probability of being essential are estimated for all genes.

::DEVELOPER

Michael A. DeJesus

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/Windows/MacOsX
Python
Scipy
Numpy

:: DOWNLOAD

MH-ESS

:: MORE INFORMATION

Citation

Michael DeJesus; Yanjia J. Zhang; Christopher M. Sassetti; Eric J. Rubin; James C. Sacchettini; Thomas R. Ioerger
Bayesian Analysis of Gene Essentiality based on Sequencing of Transposon Insertion Libraries
Bioinformatics (2013) 29 (6): 695-703.

TransposonPSI 20100822 – PSI-Blast to Mine (Retro-)Transposon ORF Homologies

TransposonPSI 20100822

:: DESCRIPTION

TransposonPSI is an analysis tool to identify protein or nucleic acid sequence homology to proteins encoded by diverse families of transposable elements. PSI-Blast is used with a collection of (retro-)transposon ORF homology profiles to identify statistically significant alignments. This method can be used to identify potential transposon ORFs within a protein set, or to identify regions of transposon homology within a larger genome sequence. This is particularly useful to identify degenerate transposon homologies within genome sequences that escape identification and masking by using RepeatMasker and an associated nucleotide library of repetitive elements. TransposonPSI has been routinely used to assist in the discovery of mobile elements across eukaryotes including protozoa, plants, fungi, and animals.

::DEVELOPER

Brian Haas @ Broad Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

TransposonPSI

:: MORE INFORMATION

TRANSPO – Searching for Transposons with known TIR

TRANSPO

:: DESCRIPTION

TRANSPO searchs transposons of Class II which are characterized by the existence of terminal inverted repeats, denoted TIR’s, that flank the transposons. Then, given the TIR, the program finds all locations at which the direct and inverse TIR approximate matches the DNA sequence and whose distance lies within a given range. Finally TRANSPO returns the following five sequences: Left Target – Left Tir – transposon – Right TIR – Right Target

::DEVELOPER

N. Santiago and Dr. J.M. Casacuberta of the CID (CSIC) and C. Herraiz, R. Goñi and Dr. X. Messeguer of the LSI (UPC).

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/ Web Browser

:: DOWNLOAD

TRANSPO

:: MORE INFORMATION