Gi Numbers To Ensembl Ids Conversion

Question

[Jayant Maini]

I am trying to convert gi numbers (sequence numbers) but i dont seem to get hold of any converter which can convert gi numbers to ensembl IDs. Can you help me to convert these gi numbers to ensembl??

Exampl of gi numbers is written below:

gi|194271429

[Khader Shameer]

Have you tried ID Mapping at Uniprot http://www.uniprot.org/ ?

Answer 1

[Pierre Lindenbaum]

Using NCBI eutils you can get an accession number for your gi

http://www.ncbi.nlm.nih.gov/dtd/NCBI_TSeq.dtd">
<TSeqSet>
<TSeq>
  <TSeq_seqtype value="protein"/>
  <TSeq_gi>194271429</TSeq_gi>
  <TSeq_accver>ACF37172.1</TSeq_accver>
  <TSeq_taxid>9606</TSeq_taxid>
  <TSeq_orgname>Homo sapiens</TSeq_orgname>
  <TSeq_defline>SNF2LT [Homo sapiens]</TSeq_defline>
  <TSeq_length>776</TSeq_length>
  <TSeq_sequence>MEQDTAAVAATVAAA(...) K</TSeq_sequence>
</TSeq>
</TSeqSet>

Then, using the ensembl mysql server, you can get the ENSEMBL-id for this protein. For example, see the SQL query in this older answer

[User 59]

Useful to know!

Answer 2

[User 59]

GI numbers aren't accessions - from the NCBI website:

GI number (sometimes written in lower case, "gi") is simply a series of digits that are assigned consecutively to each sequence record processed by NCBI. The GI number bears no resemblance to the Accession number of the sequence record.

The GI number has been used for many years by NCBI to track sequence histories in GenBank and the other sequence databases it maintains. The VERSION system of identifiers was adopted in February 1999 by the International Nucleotide Sequence Database Collaboration (GenBank, EMBL, and DDBJ).

Consequently I don't think ID mapping tools are going to cut it here. You might get somewhere with the sequence revision history tool:

http://www.ncbi.nlm.nih.gov/sviewer/girevhist.cgi?

Happy to be proved otherwise though!