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Improved TSD-motif identification
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@oushujun oushujun released this 09 Dec 06:08
· 130 commits to master since this release
v2.0
beda3bf

This version has fixed a couple minor bugs reported previously (i.e., #6, #7, #26, #28, #29).

In particular,

  1. Fix the bug 'substr sequences out of range' when the candidate locates at the boundary of a contig.
  2. Fix the bug for sometimes producing slightly different results when using both LTRharvest and LTR_FINDER inputs.
  3. Fix the bug for bias to identify TGCA motifs over non-TGCA motifs and improved TSD identification.
  4. Improve detection/filtering sensitivity for LINE/DNA transposases and plant proteins.
  5. Remove short sequences (<100bp) in the final library.
  6. Update README and citations.

The v2.0 LTR_retriever has similar high performance comparing to v1.x versions.

Rice (MSUv7) v1.x v2.0
Sensitivity 95.0% 95.3%
Specificity 95.0% 94.6%
Accuracy 95.0% 94.8%
Precision 85.4% 84.5%
Arabidopsis (TAIR10) v1.x v2.0
Sensitivity 90.7% 90.9%
Specificity 99.0% 99.0%
Accuracy 98.5% 98.5%
Precision 86.6% 86.5%
Assets 2
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