ProbeWeaver™ is a free software application provided by CombiMatrix to provide chip design and data preprocessing functions for microarray design. This application also contains features of general interest beyond the field of microarrays. ProbeWeaver™ is particularly useful for viewing and processing large lists that are common in the fields of biology and bioinformatics. See the listing below for further details.

SOFTWARE DOWNLOAD

ProbeWeaver™ -- launched with Java Web Start

ProbeWeaver™ -- Microsoft Windows installer

DOCUMENTATION

ProbeWeaver User's Manual (.pdf format)
Python ProbeWeaver Module (2kb .txt file)
Example of ProbeWeaver Module Use (1kb .txt file)

Features

• Design probes for a CombiMatrix CustomArray® microarray
• Design a CombiMatrix CustomArray® microarray with your own probes
• Choose where to place the probes on your CombiMatrix CustomArray® microarray
• Quantile and other normalization
• Genotyping analysis
• Data preprocessing and charting functions
  (histograms, scatter plots, box-and-whiskers, microarray MVA plots, etc)
• Merging of feature or probe data tables
• QC analysis for 12k and 90k feature tables
• GenBank record parsing, including CDS feature extraction
• FASTA file converter (i.e., convert to tab-delimited)
• Conversion of CombiMatrix data tables to TIGR formats for data analysis in MIDAS or MeV
• Basic operations on large lists
• BLAST output viewer
• Python scripting support
• Regular expression searching

Supported File Formats

• CombiMatrix microarray design files
• Delimited files (tab-delimited, comma-delimited / CSV, semicolon-delimited)
• GenBank flat files
• FASTA formatted sequence files from NCBI
• Microarray Imager feature data and probe data files
• ElectraSense® feature data and probe data files
• BLAST output files
• GenePix Results (*.gpr) files

System Requirements

Recommended 512M of RAM for larger list processing.