#logparanoia()
**Introduction [#v4dcb6b5]
SlideSort is fast and exact method that can find all similar pairs from a string pool in terms of edit distance.
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The input to slidesort is a set of sequences of almost equal length and a threshold of edit distance. 

From the input sequences, SlideSort exactly find all pairs within the input threshold.

SlideSort also accepts a threshold of maximum number of insertions/deletions. 
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SlideSort can find similar pairs
- within edit-distance d,
- from sequences whose length range from minimum length L to L+d
- with arbitrary gap length g.  

**Availability [#aada9741]
Goto [[Download]] page. 

**How to use SLIDESORT [#oabae487]
Goto[[Usage]] page.

**Application [#gdfadba1]
- Pre-screening of short reads assembling.
- Clustering Large-scale short reads.
-- Constructing Minimum Spanning Trees from all pairs similarity information.
--- An example of MSTs: Large MSTs of 10,000,000 short reads obtained by SLIDESORT. (Visualized by [[Walrus:http://www.caida.org/tools/visualization/walrus/]])
--- MST construction tool (SSMST) is also available in [[Download]] page. 

#ref(mst.PNG,,50%)

**Contact [#n648d166]
- shimizu-kana (AT) aist.go.jp
- Please replace (AT) by atmark.
- ( slidesort(AT)m.aist.go.jp is expired due to replacement of email system in AIST.)

**Reference [#ed7b4ba7]
- Kana Shimizu and Koji Tsuda "SlideSort:All pairs similarity search for short reads", Bioinformatics (2011) 27 (4): 464-470. [[open access article:http://bioinformatics.oxfordjournals.org/content/27/4/464.full]]

**Funding [#w2fb2c0b]
[[Grant-in-Aid for Young Scientists (22700319) by JSPS:http://kaken.nii.ac.jp/en/p/22700319]]

-------------------
Copyright © 2010-2011 [[Kana Shimizu:http://www.cbrc.jp/~shimizu/]]
Copyright © 2010-2011 [[Kana Shimizu:http://cbrc3.cbrc.jp/~shimizu/]]
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