lecture-2 - Practical Bioinformatics for Life Scientists...

Info iconThis preview shows pages 1–6. Sign up to view the full content.

View Full Document Right Arrow Icon
Practical Bioinformatics for Life Scientists Week 1, Lecture 2 István Albert Bioinformatics Consulting Center Penn State
Background image of page 1

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
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
Background image of page 2
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
Background image of page 3

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
The GFF3 specification
Background image of page 4
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)
Background image of page 5

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
Image of page 6
This is the end of the preview. Sign up to access the rest of the document.

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.

Page1 / 19

lecture-2 - Practical Bioinformatics for Life Scientists...

This preview shows document pages 1 - 6. Sign up to view the full document.

View Full Document Right Arrow Icon
Ask a homework question - tutors are online