README ====== There are three files with data about extensions to ORFs in the sequenced budding yeast strain S288C :- 1. extensns.table 2. tmpredns4extensns.out 3. alignmts4extensns.out extensns.table : This contains the sequences of all of the extensions for yeast ORFs. field #1 = chr*_ where * is the chromosome name field #2 = start coordinate for ORF field #3 = end coordinate for ORF field #4 = strand direction for ORF field #5 = name of ORF field #6 = 1 (if extension is part of an alignment to a protein sequence for >= 10 residues), -1.0 otherwise field #7 = number of transmembrane helices in extension (predicted using program TMHMM) field #8 = sequence of extension in amino acids tmpredns4extensns.out : This contains the predicted transmembrane helices for the ORF extensions: field #1 = name of ORF field #2 = length of extension field #3 = number of predicted transmembrane helices field #4 = topology of transmembrane helices, e.g., i35-57o106-128i135-157o means three helices, the first from residue 35 to 57, going from inside membrane (i) to outside (o), etc. alignmts4extensns.out : This contains information about alignments to protein sequences that involve part of an extension to an ORF: field #1 = yeast ORF name field #2 = name for aligned database sequence (this is either a SWISSPROT id or a composite name beginning with a species label, e.g., ARAB_* is an arabidopsis sequence) field #3 = start of alignment in database sequence field #4 = end of alignment in database sequence field #5 = start of alignment in yeast ORF field #6 = end of alignment in yeast ORF field #7 = alignment probability score field #8 = start of ORF extension (i.e., end of ORF sequence) field #9 = end of ORF extension