PALMA mRNA to Genome Alignments using Large Margin Algorithms
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genome align aligner sequence aligner align genome genome aligner

PALMA Description

mRNA to Genome Alignments using Large Margin Algorithms PALMA aligns two genomic sequences in an optimal way according to its underlying algorithm and trained parameters. The main Python script takes two FASTA files containing the target (e.g. a DNA sequence, part of the genome) and query sequences (e.g. a cDNA or EST sequence). PALMA creates an alignment using dynamic programming (written in c++), and returns the alignment in a psl like format. The algorithms will be the ones that will compute optimal local alignments, so if no alignment has been found it is because no alignment got a sufficiently high alignment score. Requirements: · Shogun · Python

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