I have downloaded human chromosome's data from UCSC FTP. Some part is in small alphabets and some is in large alphabets. Does it show the coding and non-coding region?
Here is an example from the file I just downloaded:
gagaatcccttgaacccgggaggcggagcttgctgtgagccgagatcgca
ccactgcactccagcctgggtgacagagccagactccgtctcaaaataaa
taaataaataaataaataaaAAAGAAAAAGGTTAATACAACATTAAAGAA
CAAGAATTAATATAGCtttttttttttttttttttttttgagacctagtc
tcactctgttgcccaggctggagggcagtggcatgatctcagctcactgc
aacctccgcctcccgggttcaggcgattctcctgcctcagcctcccgaat
aggtgggattacaggcgtgcaccaccatgcctactttttgtatttttagt
agagacggggtttcactatgttggccaggctggtgtcgaactcttgacct
caagtgatctgcctgccttggcctcccaaagtgctgggatgacaggtgtg
agccactgcacctggccTAATATAGCTTTAATAGAAAAGGAGCTAATACA
AGCTTAGAATAATAAACTTTATGCAGACTTACTGAAACAAACAGTCAATG
CAACCTTAACCAAACAGGAATTGATAACAGTTTAATAAAAAAGCTAATAC
CACTTGAATAGAATATATCTTACTACAACCTTCATAAGAAAAACAACTAA
TAcactttgggagaccgaggcaggcagatcacgaggtcaggagatcgaga
ccatggtgaaaccccgcctctactaaaaatacaaaaaaattagcctggca
Second strange thing is to see it beginning with sequence like NNNN. Like here it is:
>chrX NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN ctaaccctaaccctaaccctaaccctaaccctaaccctCTGaaagtggac ctatcagcaggatgtgggtgggagcagattagagaataaaagcagactgc
So the question is two fold:
- What is the difference between upper and lower case in nucleotide fasta sequences?
- What are the repeating
N
characters denoting?