A question regarding sequence retrieval
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
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
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Guruprasad Ananda Graduate Student Bioinformatics and Genomics The Pennsylvania State University
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pande