This directory holds supporting data for our GLAM paper: MC Frith, U
Hansen, JL Spouge and Z Weng (in press). Finding functional sequence
elements by multiple local alignment. Nucleic Acids Research.

The files ending "_50.efa" contain sets of 50 bp sequences centered on
known transcription factor binding sites. They are in "extended FASTA
format", which allows comment lines beginning with "#".

rand_hs_chr20.fa is a set of randomly chosen segments of human
chromosome 20, which were used to test GLAM's ability to align Alu
elements. rand_hs_chr20.RMout is the output of RepeatMasker applied to
this file.

golf.fa is a set of artificial sequences containing 50% G and 50% C,
with the word TATTAATTTAAA embedded once in each of them. The
alignment energy landscape of these sequences is supposed to resemble
a golf course.

The "xERE" files contain estrogen response elements that were embedded
into random sequences of varying lengths to test GLAM. The width of
these elements was determined by applying GLAM to 30 bp sequences
centered on the EREs.

SupFig1.pdf is a supplementary figure for the paper.