Hello GURU, I am having problems with retrieving the FASTA sequences in the genomic interval that I took from http://dir.nhlbi.nih.gov/Papers/lmi/epigenomes/hgtcell.aspx for the CTCF binding site. The sequence file that I am getting is empty. Please help. warm regards, Amit. Guruprasad Ananda wrote: > Hello Amit, > > The genomic sequences hosted on Galaxy are from UCSC and according to their convention repeats from RepeatMasker and Tandem Repeats Finder (with a period of 12 or less) are shown in lower case and non-repeating sequence is shown in upper case. > > Hope this answers your question. > Thanks for using Galaxy, > Guru. > > > On Mar 11, 2010, at 5:02 AM, pande wrote: > > >> Dear Galaxy, >> I have the results for the sequence retrieval for Insulator regions in the human genome and I am having difficulty in comprehending the upper and lower case associated with my sequences.I know it for sure that they are regions which do not in any way overlap with exons or introns and are that between any 2 genes. >> I am attaching a small part of the sequence file for you to see and help me. >> >> >> warm regards, >> Amit. >> >>> hg19_chr14_100364027_100364047_+ >>> >> AAGGCTTCTAATTTGGGTCT >> >>> hg19_chr14_100364319_100364339_+ >>> >> TATTTTCCCAGCAGAGGATG >> >>> hg19_chr2_21174437_21174468_+ >>> >> NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN >> >>> hg19_chr19_50965398_50965458_+ >>> >> TGTCTCAAGGGATTTAGTCACTTAAAAAAtttttttaattgatttttgat >> tttttttttt >> >>> hg19_chr19_50965141_50965201_+ >>> >> ATCCTCTCTCCCCAGGAATCACCTTCAAACCGTTCGAGTATAAGGAGCAT >> GACTTCCGGA >> >>> hg19_chr16_23597358_23597397_+ >>> >> acccctcagactcccgagtagctgggattataggcgtgc >> >>> hg19_chr11_5269210_5269281_+ >>> >> TCTTCCAAAACATCTGTTTCTGAGAAGTCCTGTCCTATAGAGGTCTTTCT >> TCCCACCGGATTTCTCCTACA >> >>> hg19_chr11_5182745_5182816_+ >>> >> ggaggaccgtaagggatataaaggttttactgaatactaagagcctgaaa >> aactgcttggctgatttgact >> >>> hg19_chr11_1947003_1947086_+ >>> >> CCAGGCCCCCTCACAGCCTTCTGCTATGAGACCCTTGAGGTGCACACAGG >> CTGGGAGCAGATGGGAGGGCTGGGGTCCCATGC >> >>> hg19_chr11_1944457_1944540_+ >>> >> GGGCCTCGTCTTTTCCCCGAAGTGTGGCCACATGGTCCTGAGGGGCCTGC >> AGGTCAGGCTCTGGGTCCTGTCTCTCTGCTTCT >> >>> hg19_chr17_38531956_38532012_+ >>> >> cctgggctcccacttcggtggcacttgaggagcccttcagcccaccgctg >> cactgt >> >>> hg19_chr17_38531327_38531376_+ >>> >> gatggtaacttcccggtggttaggttgttgccatggaaaggggcggtaa >> >>> hg19_chr3_10181494_10181542_+ >>> >> taattctttcattttttatagagacaggacctcgctatgttgcccagg >> >>> hg19_chrX_23982287_23982341_+ >>> >> ATTAGTGCATTCTTTTTCAGAAATTTTTTCTGTGCAGATATACAATCTGT >> ATAC >> >>> hg19_chrX_23982417_23982470_+ >>> >> TTAATAAACATGTCACTGCtgttgtgggtggggttgcccaggaaacagac >> tct >> >>> hg19_chr11_2112020_2112170_+ >>> >> CACCTTGCAGGGTCCCACCAAGACCACTGCAGCCTGGAATTTCCTGCTGA >> CACTGGACGTAGGAGGCCTGGAGGGCCTGCAGGGGTCAGCCAGCGCCTCC >> AGGACCCTCACTCAAACCTTGTCCCACGCCTTACCACCTTGCACCTGGTC >> _______________________________________________ >> galaxy-user mailing list >> galaxy-user(a)lists.bx.psu.edu >> http://lists.bx.psu.edu/listinfo/galaxy-user >> > > Guruprasad Ananda > Graduate Student > Bioinformatics and Genomics > The Pennsylvania State University > > > > >