lecture-11 - Practical Bioinformatics for Life Scientists...

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Practical Bioinformatics for Life Scientists Week 6, Lecture 11 István Albert Bioinformatics Consulting Center Penn State
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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
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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 ]
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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 Penn State.

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lecture-11 - Practical Bioinformatics for Life Scientists...

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