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Oct 1, 2013 (3 years and 2 months ago)

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Supplementary material:


Supplementary figure

1: Comparison of the sensitivity of the oligonucleotides designed for the custom mouse array. For each oligonucleotide set cr
eated we
plot the distribution for all oligonucleotides in the set of GC percent. The

name of the software used for design is displayed on the x axis. AOS stands for
ArrayOligoSelector.



Supplementary table

1: References of each oligonucleotide design software evaluated.


Design program

Year

References

Website

Design for a custom set o
f sequences

ArrayOligoSelector

2003

Bozdech et al. Genome Biology v4 pR9

http://arrayoligosel.sourceforge.net/

CommOligo

2005

Li et al. Nucleic Acids Research v33 p6114
-
6123

http://ieg.ou.edu/software/CommOligo2.0.rar

GoArrays

2005

Rimour et al. Bioinfo
rmatics v21 p1094

http://www.isima.fr/bioinfo/goarrays/

HPD

2005

Chung et al. Bioinformatics v21 p4092
-
4100

No website available

MPrime

2005

Rouchka et al. BMC Bioinformatics v6 p175

http://kbrin.a
-
bldg.louisville.edu/Tools/MPrime/

OliD

2003

Talla et a
l. BMC Genomics v4 p38

No website available

OligoArray

2003

Rouillard et al. Nucleic Acids Research v31 p3057

http://berry.engin.umich.edu/oligoarray2_1/

Oligodb

2002

Mrowka et al. Bioinformatics v18 p1686

http://oligodb.charite.de/

OligoFaktory

2006

Sc
hretter and Milinkovitch Bioinformatics v22 p115
-
116

http://ueg.ulb.ac.be/oligofaktory/

OligoPicker

2003

Wang et al. Bioinformatics v19 p796
-
802

http://pga.mgh.harvard.edu/oligopicker/

OligoWiz

2005

Wernersson and Nielsen Nucleic Acids Research v33 W611
-
W615

http://www.cbs.dtu.dk/services/OligoWiz2/

Oliz

2002

Chen et al. Bioinformatics v3 p27

http://www.utmem.edu/pharmacology/otherlinks/Oliz.html

Osprey

2004

Gordon et al. Nucleic Acids Research v32 e133

http://osprey.ucalgary.ca/

PICKY

2004

Chou et al.

Bioinformatics v20 p2893
-
2902

http://www.complex.iastate.edu/download/Picky/

PROBEmer

2003

Emrich et al. Nucleic Acids Research v31 p3746
-
3750

http://probemer.cs.loyola.edu/

Probesel

2002

Kaderali and Schliep Bioinformatics v18 p1340
-
9

http://www.zaik.u
ni
-
koeln.de/bioinformatik/arraydesign.html

ProbeSelect

2001

Li et al. Bioinformatics v17 p1067
-
1076

ftp://www.genetics.wustl.edu/pub/stormo/ProbeSelect/probeselect
-
src.tar

ROSO

2004

Reymond et al. Bioinformatics v20 p271
-
273

http://pbil.univ
-
lyon1.fr/ros
o/

SEPON

2004

Hornshoj et al. Bioinformatics v20 p428
-
429

http://www.agrsci.dk/hag/sepon/

YODA

2004

Nordberg et al. Bioinformatics v21 p1365
-
1370

http://pathport.vbi.vt.edu/YODA/

Tiling design

ArrayDesign

2007

Gräf et al. Bioinformatics v23 pi195
-
i204

http://www.ebi.ac.uk/~graef/arraydesign/

Lipson D

2007

Lipson et al. Bioinformatics v23 e77
-
83

No website available

MAMMOT

2006

Ryder et al. Bioinformatics v22 p883
-
884

http://www.mammot.org.uk/

OligoTiler

2006

Bertone et al. Genome Research v16 p271
-
2
81

http://tiling.gersteinlab.org/OligoTiler/oligotiler.cgi

Tileomatic

2007

Schliep et al. Algorithms in Bioinformatics p383
-
394

http://tileomatic.org/


Supplementary table

2: Parameters used to set up each of the software for the design of the custom mo
use nervous system development oligonucleotide set.


Design program

GC percent

Oligo size

Tm

Design orientation

Palindrome filter

ArrayOligoSelector

50

50




CommOligo

40
-
60

50

84
-
90

500b of the 3'


Mprime

40
-
60

50

84
-
90

500b of the 3'


OligoArray

40
-
6
0

50
-
52

84
-
90

500b of the 3'

AAAAA
-
TTTTT
-
CCCCC
-
GGGGG

OligoFaktory


50
-
52

84
-
90

500b of the 3'


OligoPicker


50

+/
-
6

3'


OligoWiz


45
-
55


3'


PICKY

40
-
60

50
-
52

+/
-
20



ROSO


50

84
-
90

500b of the 3'

AAAA
-
TTTT
-
CCCC
-
GGGG

YODA

+/
-
20

50

+/
-
6


AAAAA
-
TTTTT
-
C
CCCC
-
GGGGG