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

The following files are in FASTA format:

validation_dna.fa			(669 DNA sequences)
validation_query_noise=0.00.fa	(669 EST/cDNA sequences)
validation_query_noise=0.01.fa	(669 EST/cDNA sequences)
validation_query_noise=0.10.fa	(669 EST/cDNA sequences)
validation_query_noise=0.20.fa	(669 EST/cDNA sequences)
validation_query_noise=0.50.fa	(669 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..75,633..677,1184..1341
cagctcctgagactgctggcatgaaggggagccgtgccctcctgctggtggccctcaccc
tgttctgcatctgccgtgagtctgtgccactggggtttccagaacattcaggggtggggg
ggagtggggggtacctgagaaggtaaaatcctggcatcgggcctctgcagtgaacactcc
acctgcttctgtcacagaagtgggcaaggaccctgcagaacccgcgcccaccctactcca
ccccaaccaaggacaaagcccagctgacccaacaccagcccagtgtctcctaccccagcc
cagtccagcctgacctgacccttcaagcctctggtcataatagcctctcatcaggggaaa
tttcccccacaccaggagcttaactttccttccctggtgatcccagggaatgctgagtgg
aaattggagcagctaagattaagggggatgtggaggggtcttcgggcaaggtggagttgg
aggtgttgtggaggaagccctggggaggagaggtgggcattgaaggggaaggtctggaga
ccatggaggttggagccctggggcaggtccagggctgtggttgcaccagagtcaccctgt
cctgtcctggcatcatctcgctcgtgatgcagggatggccacaggggaggacaaaggcgg
agctggtcaagctgctggtatgagggcggcgggcaccccattttctaaagatctgcagcc
ttaccaagaccacccaacacagcacccacacagcctaccccacccacagacatccaccac
ccacagacattgcacccgcatcagccagctcaggtggacaccccagacctcctgtccacc
gagcagcccccagactccatagacctcctccccagtctgtgggatactcctccatgcaca
catgtgaacatacacagagatccaaacacaggtgcagacatgaaatgtacactgcgtgca
cacatgtataaacacgttcacacccacatgctcacactgggatatgcacacacatacatg
tgtgcacaccatcacatgtgcacacacacctcccagctgctgggaggagataggcagcaa
tatgccagacccccccccactgagggccttgcttgcctgatggagctgtggctctccact
tattgagcacagccctcttagtccacatgtgtctgccttccaggtgcaagtgctgggcag
tcaggacggtgcctaagtggacctcagacatggctcagccataggacctgccacacaagc
agccgtggacacaacgcccactaccacctcccacatggaaatgtatcctcaaaccgttta
atcaataaagcctcttccgca

and the corresponding EST sequence:
>val_noise=0.00_query1, 1..75,76..120,121..278
cagctcctgagactgctggcatgaaggggagccgtgccctcctgctggtggccctcaccc
tgttctgcatctgccggatggccacaggggaggacaaaggcggagctggtcaagctgctg
gtgcaagtgctgggcagtcaggacggtgcctaagtggacctcagacatggctcagccata
ggacctgccacacaagcagccgtggacacaacgcccactaccacctcccacatggaaatg
tatcctcaaaccgtttaatcaataaagcctcttccgca
