Tag: Repeat Family

RECON 1.05 – Identification of Repeat Families from Genomic Sequences

RECON 1.05

:: DESCRIPTION

The RECON package performs de novo identification and classification of repeat sequence families from genomic sequences. The underlying algorithm is based on extensions to the usual approach of single linkage clustering of local pairwise alignments between genomic sequences. Specifically, our extensions use multiple alignment information to define the boundaries of individual copies of the repeats and to distinguish homologous but distinct repeat element families. RECON should be useful for first-pass automatic classification of repeats in newly sequenced genomes.

::DEVELOPER

Eddy lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Mac OsX/Windows
  • Perl 
  • C Compiler

:: DOWNLOAD

 RECON

:: MORE INFORMATION

Citation:

Bao Z. and Eddy S.R. (2002)
Automated de novo Identification of Repeat Sequence Families in Sequenced Genomes.
Genome Research, 12:1269-1276.

RepeatModeler 2.0.1 – de-novo Repeat Family Identification and Modeling package

RepeatModeler 2.0.1

:: DESCRIPTION

RepeatModeler is a de-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats.

::DEVELOPER

RepeatModeler team – Institute for Systems Biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 RepeatModeler

:: MORE INFORMATION

Citation

PLoS One, 13 (3), e0193588 2018 Mar 14 eCollection 2018
Superior Ab Initio Identification, Annotation and Characterisation of TEs and Segmental Duplications From Genome Assemblies
Lu Zeng , R Daniel Kortschak , Joy M Raison , Terry Bertozzi , David L Adelson