Software Scripts and console applications MicroProbeTools

Microarray Probe Tools

Author: Roman Jaksik


This is a set of applications used analyze and process Affymetrix microarray probe sequence data. This package includes the following applications:

affy2pgc
creates a PGC file based on a probe_fasta file downloaded from the affymetrix website
brain2fasta
creates a fasta sequence file based on a probe_tab downloaded from the brainarray reposiory
brain2pgc
creates a pgc file based on a probe_tab downloaded from the brainarray reposiory
find_motif_loc
returns positions of ideal matches for each motif on the list
pgc_update_loc
updates the PGC file with probe location data including occurence of (A)n motif
probe_asign_stats
returns positions of ideal matches for each motif on the list, analyzes the ocurence of probes before and after An motif in transcript and occurence of g-quarduplexes in the probe sequence
probe_multi_transcript
calculates the amount of pfobes with different transcript assignment based on blast alignment results
probeset_gc
returns the average probeset GC composition based on individual probe GC contents and corresponding transcript gc

The example usage of each application can be viewed by running the application without any parameters.

 

Citation:
 
Jaksik R, Marczyk M, Polańska J, Rzeszowska-Wolny J. Sources of High Variance between Probe Signals in Affymetrix Short Oligonucleotide Microarrays. Sensors 2013, 14(1), 532-548

 

Python scripts: