CADO4MI (Computer Assisted Design of Oligonucleotide 4 MIcroarray) is a program for automatic design of oligonucleotides, fully customizable and accessible through a graphical user interface. For an input set of sequences, it allows parameter optimization and can combine multiple designs in distinct sequence databases.

1- Manual
The manual for CADO4MI is available here in pdf format. 
2- CADO4MI requirements
a- You will need CADO4MI sources. Please download them here.
b- CADO4MI can run on any architecture with a standard Tcl/Tk installation. You can freely download it here for any architecture (e.g. AIX, Linux, Mac OS X, Solaris and Windows) or directly here for Windows systems.
c- The database searches are performed using the BLAST program. You can download it here at the NCBI web site for any architecture.
Please read the manual for a detailed installation procedure.
3- Databases
CADO4MI requires blast-formatted nucleotide database. We provide here different versions of two transcript databases, RefSeq and UniGene for Homo sapiens. You can download the latest versions (May 2007) in fasta format and blast format (see table below).

FTP site (NCBI) Fasta (Original) Fasta (Modified) BLAST
RefSeq (release 23) RefSeq human.rna.fna.gz RefSeq.tfa.gz RefSeq_Hs.tar.gz
UniGene (build 202) UniGene Hs.seq.uniq.gz UniGene.tfa.gz UniGene_Hs.tar.gz

The original fasta files have been processed by DBFastER (free Tcl/Tk application available here) in order to improve the fasta header and simplify the blast results. DBFastER allows to keep only the Accession number and the definition from a NCBI fasta header and in option to add a prefix before the IDs (see below). It can also be used to reformat you query fasta files.

Ex: >gi|10863904|ref|NM_004239.1|Homo sapiens thyroid hormone receptor interactor 11 (TRIP11), mRNA
       >NM_004239 Homo sapiens thyroid hormone receptor interactor 11 (TRIP11), mRNA
       >RSHUM:NM_004239 Homo sapiens thyroid hormone receptor interactor 11 (TRIP11), mRNA
4- Examples
You can download here examples designed by CADO4MI.

Please cite the following article:
Muller J, Mehlen A, Vetter G, Yatskou M, Muller A, Chalmel F, Poch O, Friederich E, Vallar L.
Design and evaluation of Actichip, a thematic microarray for the study of the actin cytoskeleton.
BMC Genomics 2007 Aug 29;8(1):294.
Muller et al (2007) BMC Genomics doi: 10.1186/1471-2164-8-294
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