# README ############################################################################# #
#
# supplementary material to: 
# 
#   SNP-based validation of exonic splicing enhancers, 
#   by W.G. Faibrother, D.Holste, C.B.Burge, and P.A.Sharp 
# 
#
# 
# 1.- DATA FILES
#   - spliced alignments of CDS regions of human cDNAs
#   - no evidence of alternative splicing based on cDNA alignments
#
# 4.1M Nov 24 20:56 ALEXdb.chr1
# 3.1M Nov 24 20:53 ALEXdb.chr2
# 2.4M Nov 24 20:52 ALEXdb.chr3
# 1.5M Nov 24 20:54 ALEXdb.chr4
# 1.8M Nov 24 20:55 ALEXdb.chr5
# 2.0M Nov 24 20:54 ALEXdb.chr6
# 1.8M Nov 24 20:54 ALEXdb.chr7
# 1.3M Nov 24 20:55 ALEXdb.chr8
# 1.6M Nov 24 20:53 ALEXdb.chr9
# 1.7M Nov 24 20:51 ALEXdb.chr10
# 2.1M Nov 24 20:55 ALEXdb.chr11
# 2.1M Nov 24 20:51 ALEXdb.chr12
# 745k Nov 24 20:52 ALEXdb.chr13
# 1.2M Nov 24 20:50 ALEXdb.chr14
# 1.5M Nov 24 20:50 ALEXdb.chr15
# 1.9M Nov 24 20:50 ALEXdb.chr16
# 2.6M Nov 24 20:49 ALEXdb.chr17
# 588k Nov 24 20:50 ALEXdb.chr18
# 2.3M Nov 24 20:49 ALEXdb.chr19
# 996k Nov 24 20:49 ALEXdb.chr20
# 425k Nov 24 20:49 ALEXdb.chr21
# 867k Nov 24 20:49 ALEXdb.chr22
# 1.3M Nov 24 20:49 ALEXdb.chrX
#  85k Nov 24 20:49 ALEXdb.chrY
#
#
# ALEXdb.chr1, ALEXdb.chr2, ..., ALEXdb.chr22, ALEXdb.chrX and ALEXdb.chrY files contain 
# 117,639 internal, human exons ranging from 40-500 bp
#
#
#
# 2.- DATA STRUCTURE
# 
# >GENOA_ID:chr1.Ctg1005.G1-27:GENBANK_ID:D87742:GENE_CLS:CSG:EXON_CLS:CE:EXON_POS:I.2:EXON_LEN:162:3_SS:gtgtattcttctcaccctag|agatg:5_SS:cccag|gtaaagcctg:3_BITSCORE:8.21:5_BITSCORE:9.43
# attcttctcaccctAGagatgcaaccactgcatgaagataatttctcacgagagaagaca
# gcagaacttaatgtgcaggttcctgaagaacccacccacttggaccaacgtgtgattggg
# gacactcatgcctcagaagtgtcacagaagccaaatactgagaaagacctggacccagGT
# aaagcctgctaatt
#
# Legend:
#	>
# 	GENOA_ID .... unique transcript region (TR) identifier	| chr# .. human chromosome number
#	GENBANK_ID .. GenBank cDNA accession number		| GenBank release 134.0
#	GENE_CLS .... gene classification			|
#	EXON_CLS .... exon classification 			| CE .... constitutively spliced exon
#	EXON_POS .... exon position in TR 			| I.# ... ascending internal exon number (may have gaps)
#	EXON_LEN .... exon length (bp)				|
#	3_SS ........ 3' splice site				| 20 bp   upstream intron | 5 bp 5' end exon
#	5_SS ........ 5' splice site				| 10 bp downstream intron | 5 bp 3' end exon
#	3_BITSCORE .. 3' splice site bitscore			| Markov-order zero (weight matrix) model
#	5_BITSCORE .. 3' splice site bitscore			| Markov-order zero (weight matrix) model
#
#	16 bp upstream intron, exon, 16 bp downstream intron
#       .ic ......... inverse compliment of forward strand
#
#
# 3.- DATA ACQUISITION
#
# 	Last updated on: ......	Mon Nov 24 21:13:07 EST 2003
# 	questions to: .........	E-Mail: holste@alum.mit.edu
#				URL:	http://www.mit.edu/people/holste
#
# ################################################################################### #