RetroMap 0.021 – Characterize LTR Retroelements on a Genome Scale

RetroMap 0.021

:: DESCRIPTION

RetroMap is an application designed to help characterize LTR retroelements on a genome scale in a visually interactive manner. This is NOT a particularly great for comprehensive identification of elements found in highly nested contexts. Only the most internal element of those which are nested is likely to be identified as a complete element. The other elements will be treated as solo LTRs and internal regions depending on how you have set up your element searches. However, it is still a handy way to get a quick visual overview of the situation and create pretty figures.

::DEVELOPER

Brooke D. Peterson-Burch.

:: SCREENSHOTS

:: REQUIREMENTS

Linux /Windows/ MacOsX
Java

:: DOWNLOAD

RetroMap

:: MORE INFORMATION

Citation

Genome Biol. 2004;5(10):R78. Epub 2004 Sep 29.
Genomic neighborhoods for Arabidopsis retrotransposons: a role for targeted integration in the distribution of the Metaviridae.
Peterson-Burch BD, Nettleton D, Voytas DF.

LTR_Finder 1.0.5 – Find Full-length LTR Retrotranspsons in Genome Sequences

LTR_Finder 1.0.5

:: DESCRIPTION

LTR_Finder is an efficient program for finding full-length LTR retrotranspsons in genome sequences.

LTR_Finder Online Version

::DEVELOPER

Theoretical Life Sciences Research Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

LTR_Finder

:: MORE INFORMATION

Citation:

Zhao Xu, Hao Wang,
“LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons“,
Nucleic Acids Res. 2007 July; 35(Web Server issue): W265-W268.

MGEScan-LTR / MGEScan-non-LTR v2 – Identification of LTR/ Non-LTR Retroelements

MGEScan-LTR / MGEScan-non-LTR v2

:: DESCRIPTION

MGEScan-LTR is a de novo computational method identifies new LTR (long terminal repeat) retrotransposons without relying on a library of known elements. Specifically, the method identifies intact LTR retrotransposons by using an approximate string matching technique and protein domain analysis.

MGEScan-non-LTR is an computational approach to the identification of non-LTR retrotransposons in genomic sequences, based on a generalized hidden Markov model (GHMM), in which the hidden states represent the protein domains and linker regions encoded in the non-LTR retrotransposons, and their emission probabilities are modeled by profile hidden Markov models (for protein domains) and Gaussian Bayes classifiers (for linker regions), respectively.

::DEVELOPER

Mina Rho & Haixu Tang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

MGEScan-LTR / MGEScan-non-LTR

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2009 Nov;37(21):e143.
MGEScan-non-LTR: computational identification and classification of autonomous non-LTR retrotransposons in eukaryotic genomes.
Rho M, Tang H.