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Table 1 Feature comparison of different conversion tools (As of April 2012)

From: AbsIDconvert: An absolute approach for converting genetic identifiers at different granularities

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 â„¢

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.)

     
  1. 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.