lecture-11-handouts - 9/27/2011 Practical Bioinformatics...

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1 Practical Bioinformatics for Life Scientists Week 6, Lecture 11 István Albert Bioinformatics Consulting Center Penn State Genomic coordinates brief overview DNA two stranded and directional But there is only one coordinate system 200 300 upstream for the forward strand Standard formats use start < end even for the reverse strand The upstream region – before the 5’ end relative to the direction of transcription upstream for the reverse strand 5’ 3 5’ 3 Coordinate systems 0 based 0 , 1, 2, … 9 1 based 1, 2, 3, … 10 Typically 0 based are non-inclusive 10:20 [ 10, 20 ) 1 based include both ends 10:20 [ 10, 20 ] Comparing coordinate systems 0 based indexing Third element : 2 First ten : 0, 10 Second ten : 10, 20 Third ten : 20, 30 One base long : start, start +1 Size of interval : end start Empty interval : start, start Five elements starting at 1000 1000, 10000 + 5 1 based indexing Third element : 3 First ten : 1, 10 Second ten : 11, 20 Third ten : 21, 30 One base long : start, start Size of interval : end - start + 1 Empty interval : ? Five elements
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This note was uploaded on 02/29/2012 for the course BMMB 597D taught by Professor Istvanalbert during the Fall '11 term at Pennsylvania State University, University Park.

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lecture-11-handouts - 9/27/2011 Practical Bioinformatics...

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