What Is 3-P And 5-P Flanking Sequence? How To Find Them Using Pygr?

Question

[Use]

For example,

>>> hg17=worldbase.Bio.Seq.Genome.HUMAN.hg17()

>>> len(hg17)
46
>>> hg17.keys()
['chr6_random', 'chr19_random', 'chr8_random', 'chrY', 'chrX', 'chr13', 'chr12', 'chr11', 'chr15_random', 'chr17', 'chr16', 'chr15', 'chr14', 'chr19', 'chr18', 'chrM', 'chr1_random', 'chr13_random', 'chr3_random', 'chr6_hla_hap2', 'chr9_random', 'chr22_random', 'chr10', 'chr4_random', 'chr18_random', 'chr2_random', 'chr22', 'chr20', 'chr21', 'chr10_random', 'chr6_hla_hap1', 'chr7', 'chr6', 'chr5', 'chr4', 'chr3', 'chr2', 'chr1', 'chr7_random', 'chrX_random', 'chr9', 'chr8', 'chr16_random', 'chr5_random', 'chr17_random', 'chr12_random']

>>> chr1=hg17['chr1']

>>> len(chr1)
245522847

>>> s=chr1[100000000:100001000]

>>> len(s)
1000

>>> repr(s)
'chr1[100000000:100001000]'

>>>print s
ATTCAGGCAATGTTGACTTCATTAGTGTTGACAGAAAATAAGCATAAAAATGCAAAACATTGTTGGCTTAACCTGAATATACCTGCATTACCTATTATTAACCAGTTTGTGTTGCCAAAAGACTTATTCCTTGGCATTAAAATGGAGCACTTAAAAATATTTCTAAAAAGCAAATGCCCACA....

How to find the 5pflank and 3pflank of a chromosome location?

[Sean Davis]

Are you starting from the sequence (like "s") or from chromosome locations? In other words, what are the inputs from which you want to get flanking sequence?

[Use]

I want to get 5p_flank and 3p_flank sequence of a chromosome location. Sorry for the confusion..

Answer 1

[Sean Davis]

Assuming that your locations are relative to the positive strand, the 5p_flank is obtained by subtracting from your location. In other words, if you want 1000 bp of 5p_flanking sequence and your location is at X, your 5p_flanking sequence will be chr1[X-1000:X-1]. For the 3p_flank, simply add 1000 to the end location.