README file for validation.tar.gz
Uta Schulze, 03-Sep-2008

The following files are in FASTA format:

validation_dna.fa			(2257 DNA sequences)
validation_query_noise=0.00.fa	(2257 EST/cDNA sequences)
validation_query_noise=0.01.fa	(2257 EST/cDNA sequences)
validation_query_noise=0.10.fa	(2257 EST/cDNA sequences)
validation_query_noise=0.20.fa	(2257 EST/cDNA sequences)
validation_query_noise=0.50.fa	(2257 EST/cDNA sequences)

The description lines in each FASTA file contain an identifier. In addition, the headers in the files validation_dna.fa and validation_query_noise=0.00.fa contain the true exon boundaries created by an alignment between a DNA sequence with its corresponding EST/cDNA (query) sequence.
They are written the following way: "exon1_start..exon1_end,exon2_start..exon2_end,exon3_start..exon3_end"

For example a DNA sequence is:
>val_dna1, 1..249,637..670,724..976
atgaccgataaaataggagaacgattggatgagatcatcggtttcgagctcagcaatggt
actaaaaatcgtgagaaaatcaccaccgaactatgttcacaatttttggagtcattgagt
gaagaaattgagaaaaatggtgaagatgtggaagaagacgaaggagccaatgaacagcca
tttgaggataaattgaatttaattgggaaaatccaacaatatttgaccaatgcaaagatg
gagaaagaagtaagtcaaatgttcttatttattcaataagtttaaaacatatacagtaat
tttaaaggatttctgctttcaactaagctatagaatccatataatttggagttagtaaca
taaaaacagcttaaataattaaataacatcttgtttttttgtttaaacaatacaactagc
tccaatgaagctgcatcggatactgaatttttcaatttaacaaacaattttttcttttat
aagctttatgacgaagtgtttacatagagtcgagtacactcatttccaattgacacccag
aagagataatttgttctaggagtttttttcagagtgtcttatgataaaactgataagaaa
aaataattttcatgattaatcatattctatttacagttcaacagacgcaatttttcaaat
tcattggaaggtaaattaactgttttttgaacaccaacaaactcatttaatttcaaattt
cagaaaagatggcatctctgagtgtaactaaaaaatactcgatcaatcttgggactctcc
tcttccttttccttgactactatctggatgttatttcccttgaaaaagagtatttggaaa
ttggaactggagaatctcttattaaacttgacattggactgaccaacaagaacattttat
caattagtgacatctttgacgatcatgttccaggagaaagagtcaacgatactgttatgt
tgaagaaaattttcaa

and the corresponding EST sequence:
>val_noise=0.00_query1, 1..249,250..283,284..536
atgaccgataaaataggagaacgattggatgagatcatcggtttcgagctcagcaatggt
actaaaaatcgtgagaaaatcaccaccgaactatgttcacaatttttggagtcattgagt
gaagaaattgagaaaaatggtgaagatgtggaagaagacgaaggagccaatgaacagcca
tttgaggataaattgaatttaattgggaaaatccaacaatatttgaccaatgcaaagatg
gagaaagaattcaacagacgcaatttttcaaattcattggaagaaaagatggcatctctg
agtgtaactaaaaaatactcgatcaatcttgggactctcctcttccttttccttgactac
tatctggatgttatttcccttgaaaaagagtatttggaaattggaactggagaatctctt
attaaacttgacattggactgaccaacaagaacattttatcaattagtgacatctttgac
gatcatgttccaggagaaagagtcaacgatactgttatgttgaagaaaattttcaa
