PALMA | Tool name | PALMA |
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| URL | http://www.fml.tuebingen.mpg.de/raetsch/suppl/palma |
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| Important features | 1. A novel approach based on large margin learning that combines accurate splice site predictions with common sequence alignment techniques.
2. By solving a convex optimization problem, algorithm called PALMA tunes the parameters of the model such that true alignments score higher than other alignments.
3. It identifies the intron boundaries as well as boundaries of the optimal local alignment.
4. This method also demonstrates robustness to mutations, insertions and deletions, retaining accuracy even at high noise levels. |
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| Citations | Schulze U, Hepp B, Ong CS, Ratsch G.
PALMA: mRNA to genome alignments using large margin algorithms.
Bioinformatics. 2007 Aug 1;23(15):1892-900. Epub 2007 May 30.
PMID: 17537755 |
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| Year of publication | 2007 |
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| Rank by usage frequency | 97 |
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| Comments | |
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| Function | RNA seq alignment |
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| Category | Free, Downloadable |
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| License | GPL v2 |
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| Status | |
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| Input file format | FASTA |
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| Output file format | PSL-like |
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| Operating system | Mac OS X and Linux |
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| Operating language | python and c++ |
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