Table 1.
Feature comparison of different conversion tools (As of April 2012)
|
Name |
Caters |
Intervals |
Seqs |
ID |
Annot. |
Linkout |
Query |
Input |
Output |
Annot. |
Basis of |
Output |
Organisms |
Availability |
Last |
||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| to | to IDs | to IDs | lookup | View | mode | conversion | format | update | |||||||||
|
DAVID |
probes, genes, |
|
✓ |
✓ |
✓ |
✓ |
batch |
select one |
select |
S, F |
custom generated |
html, txt |
NA |
web,API, |
Sep, 2009 |
||
| |
prots. |
|
|
|
|
|
one |
|
|
|
|
|
⇓ |
EASE, |
|
||
|
Babelomics |
probes, genes, |
|
|
|
✓ |
✓ |
batch |
select one |
select |
S, F |
custom generated |
html, txt |
11 org. |
web |
Sep, 2009 |
||
| |
prots. |
|
|
|
|
|
multiple |
|
|
|
|
|
|
|
|
||
|
g:Convert |
genes , prots. and |
|
|
|
|
|
batch |
select one |
select |
S, F |
Ensembl |
html, txt, xls |
H, M, R, O |
web |
Jun, 2011 |
||
| |
probes |
|
|
|
|
|
one |
|
|
|
|
|
|
|
|
||
|
HMS and IC |
genes, prots. and |
|
|
|
✓ |
✓ |
batch |
select one |
select |
S, F |
corr. files |
html, txt |
H, M, O |
web, ⇓ |
current |
||
| |
bio. molecules |
|
|
|
|
|
one |
|
|
|
|
|
|
|
|
||
|
Synergizer |
probes, genes and |
|
|
|
|
|
batch |
select one |
select |
S |
Peg/custom |
html, xls |
H, M, R, O |
web, API |
May, 2011 |
||
| |
Prots. |
|
|
|
|
|
one |
|
|
|
generated |
|
|
|
|
||
|
Clone/Gene |
genes and |
|
|
|
|
✓ |
batch |
select one |
select |
S, F |
Ensembl |
html, txt, xls |
H, M, R |
web |
Apr, 2008 |
||
| |
prots. |
|
|
|
|
|
multiple |
|
|
|
|
|
|
|
|
||
|
ID Converter |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
||
|
MADGene |
probes, genes, |
|
|
|
|
✓ |
batch |
NA |
select |
S, F |
MADGene link |
html, xls |
H, M, R, O |
web, open |
Aug, 2009 |
||
| |
trans. |
|
|
|
|
|
multiple |
|
|
|
|
|
(17 org.) |
source |
|
||
|
GATExplorer |
Affy expression & |
|
✓ |
|
✓ |
✓ |
single |
probes |
genes, |
S |
Ensembl |
html |
H, M, R |
web, ⇓ |
Mar, 2010 |
||
| |
exon arrays |
|
|
|
|
|
trans. |
|
|
|
|
|
|
|
|
||
|
NetAffx™ |
genes, prots., |
|
|
|
✓ |
✓ |
batch |
select one |
select |
S, F |
UniGene, LocusLink |
html, txt |
H, M, R, O |
web |
CND |
||
| |
probes, other |
|
|
|
|
|
one |
|
|
|
|
|
|
|
|
||
|
PLANdbAffy |
Affy expression |
|
|
|
✓ |
✓ |
single |
Affy, Hugo,Ens |
Affy, Hugo, |
S |
RefSeq |
html |
H |
web, ⇓ |
May, 2009 |
||
| |
arrays |
|
|
|
|
|
Ens. |
|
|
|
|
|
|
|
|
||
|
probeMatchDB |
probes, cDNA, |
|
|
✓ |
|
✓ |
batch |
select one |
select |
S |
UniGene, Homologene |
html |
H, M, R |
web |
2006 |
||
| |
EST, gene, prots. |
|
|
|
|
|
one |
|
|
|
|
|
|
|
|
||
|
Uniprot |
genes and |
|
|
|
✓ |
✓ |
batch |
genes or prots. |
prots. or |
S, F |
UniProt ID |
html |
NA |
web, API, ⇓ |
Jul, 2011 |
||
| |
prots. |
|
|
|
|
|
gene |
|
|
|
|
|
|
|
|
||
|
Onto- |
Affy, uniGene clusters, |
|
|
|
|
✓ |
batch |
select one |
select |
S, F |
RefSeq, Entrez |
html, email |
H, M, R, O (58 org.) |
web |
May, 2009 |
||
|
Translate |
Acc num |
|
|
|
|
|
one |
|
|
|
|
|
|
|
|
||
|
AliasServer |
Affy, genes, |
|
|
|
|
✓ |
batch |
select one |
select multiple |
S |
custom generated |
html, txt |
Not Available |
Not Available |
CND |
||
| |
prots. |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
||
|
MatchMiner |
Affy, |
|
|
✓ |
|
|
batch |
select one |
choose from |
S |
custom generated |
Email (txt,xls) |
H, M |
web |
Sep. 2006 |
||
| |
genes |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
||
|
GeneMerge |
genes and |
|
|
|
|
|
batch |
select one |
NA |
S, F |
corr. files |
html |
5 org. |
web |
Apr, 2007 |
||
| |
prots. |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
||
|
BioMart |
genes, prots., |
|
|
|
✓ |
✓ |
NA |
select one |
select multiple |
S, F |
NA |
html, txt, xls |
H, M, R, O |
web, API, ⇓ |
depends on DB |
||
| |
probes, other |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
||
|
BridgeDb |
probes, genes, |
|
|
NA |
NA |
✓ |
NA |
NA |
NA |
S, F |
Ensembl, other |
NA |
36 org. |
open source |
May, 2011 |
||
| |
prots., metabolites |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
||
|
AbsIDconvert |
genes, trans., |
✓ |
✓ |
✓ |
✓ |
✓ |
batch |
select one |
select multiple |
S |
Genomic Sequence |
html, txt |
H, M, R, O |
web, ⇓VM |
Dec, 2011 |
||
| seqs., probes | (53 org.) |
aAbbreviations: Annot. View: Custom Annotation view, Annot.: Annotation (S: Structural annotation, F: Functional annotation), org.: Organisms (H: Human, M: Mouse, R: Rat, O: others), prots: proteins, Affy: Affymetrix®;, trans: transcripts, seqs: sequences, Ens.: Ensembl, corr: correspondence, acc: accession, bio: biological, NA: Not Applicable, CND: Could not determine, ⇓:download Knowledgebase, VM: Virtual Machine.