Initial import of genesplicer, one of the many packages provided by

brook at biology dot nmsu dot edu and his team at NMSU.

GeneSplicer is a  fast, flexible system for detecting splice sites in the
genomic DNA of various eukaryotes. The system has been trained and tested
successfully on Plasmodium falciparum (malaria), Arabidopsis thaliana, human,
Drosophila, and rice.

1 files changed, 148 insertions, 0 deletions

diff --git a/biology/genesplicer/PLIST b/biology/genesplicer/PLIST
new file mode 100644
index 00000000000..d3f97e4560c
--- /dev/null
+++ b/biology/genesplicer/PLIST
@@ -0,0 +1,148 @@
+@comment $NetBSD: PLIST,v 1.1.1.1 2003/09/30 01:57:09 jschauma Exp $
+bin/genesplicer
+share/examples/genesplicer/arabidopsis/acc1.mar
+share/examples/genesplicer/arabidopsis/acc15
+share/examples/genesplicer/arabidopsis/acc16
+share/examples/genesplicer/arabidopsis/acc22
+share/examples/genesplicer/arabidopsis/acc24
+share/examples/genesplicer/arabidopsis/acc25
+share/examples/genesplicer/arabidopsis/acc26
+share/examples/genesplicer/arabidopsis/acc6
+share/examples/genesplicer/arabidopsis/acc7
+share/examples/genesplicer/arabidopsis/acc8
+share/examples/genesplicer/arabidopsis/config_file
+share/examples/genesplicer/arabidopsis/don1.mar
+share/examples/genesplicer/arabidopsis/don13
+share/examples/genesplicer/arabidopsis/don14
+share/examples/genesplicer/arabidopsis/don19
+share/examples/genesplicer/arabidopsis/don20
+share/examples/genesplicer/arabidopsis/don23
+share/examples/genesplicer/arabidopsis/don24
+share/examples/genesplicer/arabidopsis/don7
+share/examples/genesplicer/arabidopsis/don8
+share/examples/genesplicer/arabidopsis/exons.dat
+share/examples/genesplicer/arabidopsis/f.acc
+share/examples/genesplicer/arabidopsis/f.don
+share/examples/genesplicer/arabidopsis/outex
+share/examples/genesplicer/arabidopsis/outin
+share/examples/genesplicer/arabidopsis/score_ex.acc
+share/examples/genesplicer/arabidopsis/score_ex.don
+share/examples/genesplicer/arabidopsis/score_in.acc
+share/examples/genesplicer/arabidopsis/score_in.don
+share/examples/genesplicer/arabidopsis/seqs
+share/examples/genesplicer/drosophila/acc1.mar
+share/examples/genesplicer/drosophila/acc2
+share/examples/genesplicer/drosophila/acc3
+share/examples/genesplicer/drosophila/acc4
+share/examples/genesplicer/drosophila/config_file
+share/examples/genesplicer/drosophila/don1.mar
+share/examples/genesplicer/drosophila/don2
+share/examples/genesplicer/drosophila/don4
+share/examples/genesplicer/drosophila/don5
+share/examples/genesplicer/drosophila/don6
+share/examples/genesplicer/drosophila/exons.dat
+share/examples/genesplicer/drosophila/f.acc
+share/examples/genesplicer/drosophila/f.don
+share/examples/genesplicer/drosophila/false.filter.acc
+share/examples/genesplicer/drosophila/false.filter.don
+share/examples/genesplicer/drosophila/false.nofilter.acc
+share/examples/genesplicer/drosophila/false.nofilter.don
+share/examples/genesplicer/drosophila/outex
+share/examples/genesplicer/drosophila/outin
+share/examples/genesplicer/drosophila/score_ex.acc
+share/examples/genesplicer/drosophila/score_ex.don
+share/examples/genesplicer/drosophila/score_in.acc
+share/examples/genesplicer/drosophila/score_in.don
+share/examples/genesplicer/drosophila/seqs
+share/examples/genesplicer/fasta.example
+share/examples/genesplicer/fasta.results
+share/examples/genesplicer/human/acc1.mar
+share/examples/genesplicer/human/acc13
+share/examples/genesplicer/human/acc14
+share/examples/genesplicer/human/acc19
+share/examples/genesplicer/human/acc20
+share/examples/genesplicer/human/acc25
+share/examples/genesplicer/human/acc26
+share/examples/genesplicer/human/acc32
+share/examples/genesplicer/human/acc33
+share/examples/genesplicer/human/acc34
+share/examples/genesplicer/human/acc7
+share/examples/genesplicer/human/acc8
+share/examples/genesplicer/human/chgd.fasta
+share/examples/genesplicer/human/config_file
+share/examples/genesplicer/human/don1.mar
+share/examples/genesplicer/human/don10
+share/examples/genesplicer/human/don15
+share/examples/genesplicer/human/don16
+share/examples/genesplicer/human/don19
+share/examples/genesplicer/human/don2
+share/examples/genesplicer/human/don20
+share/examples/genesplicer/human/don23
+share/examples/genesplicer/human/don24
+share/examples/genesplicer/human/don9
+share/examples/genesplicer/human/embls.seq
+share/examples/genesplicer/human/exons.dat
+share/examples/genesplicer/human/exons.list
+share/examples/genesplicer/human/f.acc
+share/examples/genesplicer/human/f.don
+share/examples/genesplicer/human/outex
+share/examples/genesplicer/human/outin
+share/examples/genesplicer/human/score_ex.acc
+share/examples/genesplicer/human/score_ex.don
+share/examples/genesplicer/human/score_in.acc
+share/examples/genesplicer/human/score_in.don
+share/examples/genesplicer/human/seqs
+share/examples/genesplicer/malaria/acc1.mar
+share/examples/genesplicer/malaria/config_file
+share/examples/genesplicer/malaria/don1.mar
+share/examples/genesplicer/malaria/f.acc
+share/examples/genesplicer/malaria/f.don
+share/examples/genesplicer/malaria/false.filter.acc
+share/examples/genesplicer/malaria/false.filter.don
+share/examples/genesplicer/malaria/false.nofilter.acc
+share/examples/genesplicer/malaria/false.nofilter.don
+share/examples/genesplicer/malaria/score_ex.acc
+share/examples/genesplicer/malaria/score_ex.don
+share/examples/genesplicer/malaria/score_in.acc
+share/examples/genesplicer/malaria/score_in.don
+share/examples/genesplicer/pyoelii/acc1
+share/examples/genesplicer/pyoelii/acc1.mar
+share/examples/genesplicer/pyoelii/acc2
+share/examples/genesplicer/pyoelii/config_file
+share/examples/genesplicer/pyoelii/don1
+share/examples/genesplicer/pyoelii/don1.mar
+share/examples/genesplicer/pyoelii/don2
+share/examples/genesplicer/pyoelii/f.acc
+share/examples/genesplicer/pyoelii/f.don
+share/examples/genesplicer/pyoelii/outex
+share/examples/genesplicer/pyoelii/outin
+share/examples/genesplicer/pyoelii/score_ex.acc
+share/examples/genesplicer/pyoelii/score_ex.don
+share/examples/genesplicer/pyoelii/score_in.acc
+share/examples/genesplicer/pyoelii/score_in.don
+share/examples/genesplicer/readme
+share/examples/genesplicer/rice/acc1.mar
+share/examples/genesplicer/rice/config_file
+share/examples/genesplicer/rice/don1.mar
+share/examples/genesplicer/rice/exons.dat
+share/examples/genesplicer/rice/f.acc
+share/examples/genesplicer/rice/f.don
+share/examples/genesplicer/rice/score_ex.acc
+share/examples/genesplicer/rice/score_ex.don
+share/examples/genesplicer/rice/score_in.acc
+share/examples/genesplicer/rice/score_in.don
+share/examples/genesplicer/rice/seqs
+share/examples/genesplicer/training_data_sets/Arabidopsis/exons.dat.nohomologs
+share/examples/genesplicer/training_data_sets/Arabidopsis/seqs.nohomologs
+share/examples/genesplicer/training_data_sets/Human/exons.dat.nohomologs
+share/examples/genesplicer/training_data_sets/Human/seqs.nohomologs
+@dirrm share/examples/genesplicer/training_data_sets/Human
+@dirrm share/examples/genesplicer/training_data_sets/Arabidopsis
+@dirrm share/examples/genesplicer/training_data_sets
+@dirrm share/examples/genesplicer/rice
+@dirrm share/examples/genesplicer/pyoelii
+@dirrm share/examples/genesplicer/malaria
+@dirrm share/examples/genesplicer/human
+@dirrm share/examples/genesplicer/drosophila
+@dirrm share/examples/genesplicer/arabidopsis
+@dirrm share/examples/genesplicer