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

The following files are in FASTA format:

test_dna.fa			(4358 DNA sequences)
test_query_noise=0.00.fa	(4358 EST/cDNA sequences)
test_query_noise=0.01.fa	(4358 EST/cDNA sequences)
test_query_noise=0.10.fa	(4358 EST/cDNA sequences)
test_query_noise=0.20.fa	(4358 EST/cDNA sequences)
test_query_noise=0.50.fa	(4358 EST/cDNA sequences)

The description lines in each FASTA file contain an identifier. In addition, the headers in the files test_dna.fa and test_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:
>test_dna1, 1..140,188..223,618..1097
ttcaggtatacctagttcagtctagctccaagtctcctgatgtgcgttgacgttccatgt
gaaaactgcattgttcgcaatgacgggctccggctgaaatgttctgaatgtgctgaagga
tcctcgaagctattcccaaggttagttgattatttgtgttcgatatcaataaatccataa
tttacagacaaaaccgtcaacactcaatggagggcatattaaggttagtttttgccgttt
gtactacgtttccagactccaaagtcttagtgtgtacctttaagtttacagtaaccctcg
taatttatattctctcttcgtgtccgtgtatcattttagtttttcaataaatagactctt
tcgagagaaaatgccatatgagaatgggatactgtacttcttaaaactcgtacttaaaga
atcatgagtccgttctaatgggttctgtcaaaaacagaaaacacatttaattttagaatt
aataaaaaatctactttccttcgtggcaagacccttccaaaccaaatcatgcgcctttaa
gtgtgcgtttcagaaaaaagaattataataactgttttgaaaaaataccagaaagttaaa
actgcaaatcttttcagggagctcaaagcctgttcaatccagaaactgctgcagacttct
tcttcaacaaagatggttccaagaaaatcaaccggatacccattttctactgtgaataca
gtcaaaaacgtggaccaaccatggcgaacaaccttcgggaagtggacagaaaactgaatt
caaatatctatccgagatgtgattatgaggagatttatttgttggaaggaggttataaaa
acttttacgctttcacgcggggattagagaaggaacaaagagtacaactctgtgagccag
ataattatgtaatcatgtttgatgatcgttataaggctgagcttcggaagcaccagttcc
ataagaagaatgtttcgaagccaatgaagaaatggagttcaacaacatctgtgatatcta
ttctaacaacttctggaactcgtatttcgacacttcgtcagacatgtgatcccatccatg
agcacgatgcgcattaa

and the corresponding EST sequence:
>test_noise=0.00_query1, 1..140,141..176,177..656
ttcaggtatacctagttcagtctagctccaagtctcctgatgtgcgttgacgttccatgt
gaaaactgcattgttcgcaatgacgggctccggctgaaatgttctgaatgtgctgaagga
tcctcgaagctattcccaagacaaaaccgtcaacactcaatggagggcatattaagggag
ctcaaagcctgttcaatccagaaactgctgcagacttcttcttcaacaaagatggttcca
agaaaatcaaccggatacccattttctactgtgaatacagtcaaaaacgtggaccaacca
tggcgaacaaccttcgggaagtggacagaaaactgaattcaaatatctatccgagatgtg
attatgaggagatttatttgttggaaggaggttataaaaacttttacgctttcacgcggg
gattagagaaggaacaaagagtacaactctgtgagccagataattatgtaatcatgtttg
atgatcgttataaggctgagcttcggaagcaccagttccataagaagaatgtttcgaagc
caatgaagaaatggagttcaacaacatctgtgatatctattctaacaacttctggaactc
gtatttcgacacttcgtcagacatgtgatcccatccatgagcacgatgcgcattaa
