> Hi,
> I am trying to write a C program that can chop up the
> ALUs sequences from a file and leave ALUless sequence only. I
> would appreciate some explanation on the use of repe on the
> file. Below is an example of the use of repe.
>>> ID luc13.00026
> EN luc13.00026
> LN luc13.00026
> LT PLN
> QR 1018
> SQ
> cgagaaaca cccaagaatg atcaataaaa aaataataat taaaaaaaaa aaagaaaaaa
> a aaagaaaa gaaaccacag tggccgattg cagtggctca ctcctgtaat cccagcactt
> tg ggaggcc gaggcgggca gatcacgagg tcaggagatc gagaccattc tggctaacac
> ggt gaaacc ccatctctat taaaaataca aaaaaaaaat agccgggcgt ggtggtggtt
> gcct gtagt cccagctact caggaggctg aggcaggaga atggcgtgaa cctgagaggc
> ggagg ttca gtgagctgag accctgccac tgcactccag cctgagtgac agagcgggac
> tctgtc tca aaaaaaaaaa aaaaaacaca cagcttagtt ttcagtgact ccaaattagg
> aaaatga aa aaaaagaagg aaaaaaattg aaaacttaat ttgaagactt gtagccaaga
> aaaattca t tccaaactgt agaaaatcat aaaaattgga agcaaacaaa caaaaaaaca
> gttaagact agaatctaac aacaggtgaa cattcgtttt gaaacatgat tttattctct
> ctccaatttc ccattttac taaagacaaa tcatggtatg acttgtttgc ttattatact
> tggcctaaat a tttgtata cagtgcagca agaataattt attttgtccc ataagaggaa
> tctcaggtaa ga cttttta aagccctgcc cagccatgga tttgtgccat caaataccca
> tgagttggat gga atttcc tctcctttca agttccaaga taaacataaa cctggggcct
> ctgtgcctgt caga aagtg acatcctttt ttttttgatc aggctagtct tgaattcctg
> acctcaggtg atcct cccg cgttggcctc ccaaagtgct gggattacag gcatgagcca
> ccactcctgg ccccag aaa gtgacattct ttacttacca caggtaagaa atcctgt
> //
> TG ALUS + 81..370
> TG 0.913
> TG ALUS - 841..1000
> TG 0.741
>>>> I would be grateful if anyone can help on the following
queries:
>> 1) in the above example the sequence is 1000bp. Does the good
> sequence lie between base 371-840?
>> 2) What does ALUS + and ALUS - exactly mean?
>> 3) What do the numbers 0.913 and 0.741 mean. I noticed that
> anything with is 0.5 and below is passed as non-ALU sequence,
> am I right?
>>> Thanks for your help.
>> rifat
>>
