lecture-2-handouts

lecture-2-handouts - 8/25/2011 Practical Bioinformatics for...

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8/25/2011 1 Practical Bioinformatics for Life Scientists Week 1, Lecture 2 István Albert Bioinformatics Consulting Center Penn State Biological file formats Each file format is a statement on 1. Information the type of knowledge that is stored in it 2. Optimization the type of operations that are easy to perform Tabular formats Most common formats are tab-separated and column oriented files First format we deal with will be the GFF Generic Feature Format (search for GFF to see the specification) http://www.sequenceontology.org/gff3.shtml The GFF3 specification
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8/25/2011 2 GFF format Search for GFF3 http://www.sequenceontology.org/gff3.shtml Tab separated with 9 columns. Missing attributes may be replaced with a dot . 1. Seqid (usually chromosome) 2. Source (where is the data coming from) 3. Type (usually a term from the sequence ontology) 4. Start (interval start relative to the seqid) 5. End (interval end relative to the seqid) 6. Score (the score of the feature, a floating point number)
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lecture-2-handouts - 8/25/2011 Practical Bioinformatics for...

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