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update readme to add references for ISEScan
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xiezhq committed Jul 7, 2017
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ISEScan was developed using Python3. It 1) scanes genome (or metagenome) in fasta format; 2) predicts/translates (using FragGeneScan) genome into proteome; 3) searches the pre-built pHMMs (profile Hidden Markov Models) of transposases (two files shipped with ISEScan; clusters.faa.hmm and clusters.single.faa) against the proteome and identifies the transposase gene in genome; 4) then extends the identified transposase gene into the complete IS (Insertion Sequence) elements based on the common characteristics shared by the known IS elements reported by literatures and database; 5) finally reports the identified IS elements in a few result files (a list of IS elements, sequences of IS elements in fasta format, annotation file in GFF3 format).
## References:
Zhiqun Xie, Haixu tang. ISEScan: automated identification of Insertion Sequence Elements in prokaryotic genomes. Bioinformatics, 2017[https://doi.org/10.1093/bioinformatics/btx433](https://doi.org/10.1093/bioinformatics/btx433).
Zhiqun Xie, Haixu tang. ISEScan: automated identification of Insertion Sequence Elements in prokaryotic genomes. Bioinformatics, 2017. ([https://doi.org/10.1093/bioinformatics/btx433](https://doi.org/10.1093/bioinformatics/btx433))

## Installation

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