Hi, Using the interval file which you used to fetch fasta sequences, you'll be able to fetch human-chimp alignments. Please use "Extract pairwise MAF blocks" tool under "Fetch alignments" and select "hg18,panTro2" as MAF source. If the MAF source field is empty, please make sure that the database build of your input interval file is set to 'hg18'. Please feel free to email us if you have any further questions. Thanks, Guru. On Mar 18, 2010, at 9:02 AM, pande wrote:

Thank you so much for your quick response..........and may I take the liberty of asking you another question ? If I have sequences from the human genome and I want to see their alignment with the Chimp genome are there such pre-computed sets available at the UCSC genome browser or Galaxy ? People have told me but till now I have not been successful.

Please help me.

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@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user

Guruprasad Ananda Graduate Student Bioinformatics and Genomics The Pennsylvania State University

Guruprasad Ananda Graduate Student Bioinformatics and Genomics The Pennsylvania State University