repe and ALU sequence file <fwd>

Rifat Hamoudi rifat at icr.ac.uk
Thu Mar 27 07:13:26 EST 1997


> 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
>  
> 






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