getting genomic coordinates from gene accesion information

mathew · 03-16-2011, 06:40 PM

I have list of gene accession numbers (e.g AY.... - Chr no start --- and stop ---).
Is there any way that I can get genomic location of these regions in Hg18.
I have tried USCS geneom browser Table that will not work.
Thanks

Bert · 03-17-2011, 07:43 AM

Hello Mathew,

From the title and content of your post it's not clear to me what you want to accomplish .... What data do you exactly have and what data do you want to retrieve?

Cheers,
Bert

mathew · 03-17-2011, 07:59 AM

What I have is Genebank accession Id (like AY293855) - Chr no (6 ) and start (140600) and stop (1407890) so I want to find out corresponding genomic coordinates in Hg18.
Thanks Bert

Bert · 03-17-2011, 08:35 AM

Mathew,

It's still not clear to me what your coordinates represent. Relative to which sequence are they?

And how many of these ID's do you have?

Cheers,
Bert

Pankaj kumar · 03-17-2011, 08:40 AM

Hi,
check the ucsc genome browser.
http://genome.ucsc.edu/cgi-bin/hgLiftOver
You need to give input as chr# start_position end_position
select your assembly and you are done.
Pankaj

Bert · 03-17-2011, 08:48 AM

What Matthew has are not genomic coordinates as far as I can see .... AY293855 is a sequence from the IGF2R gene, and that is located in GRCh37 (hg19) at position 160390131-160534539 (http://www.ensembl.org/Homo_sapiens/...0131-160534539).

Cheers,
Bert

Pankaj kumar · 03-17-2011, 08:51 AM

Hi Bert,
He has genomic co-ordinate.
see "Chr no (6 ) and start (140600) and stop (1407890)"

Bert · 03-17-2011, 09:01 AM

Pankaj,

Please read my reply carefully. Mathew has a GenBank / EMBL / DDBJ ID and some coordinates. If you would look up the ID (AY293855), you would see that this is the sequence for the human IGF2R gene (http://www.ebi.ac.uk/ena/data/view/AY293855). When you then would look up where this gene is located in GRCh37 (hg19) you would see that it is on chromosome 6 at position 160390131-160534539 (http://www.ensembl.org/Homo_sapiens/...0131-160534539). Now, that are quite different numbers from 140600-1407890, right? So, the coordinates Mathew has cannot be genomic coordinates. I suspect they are relative to e.g. a clone or so.

Cheers,
Bert

mathew · 03-17-2011, 02:26 PM

Bert,
You are right I have locations which have been published in paper with the corresponding gene bank accession # (Ay...,AC.. etc) I only have handful of these. I have sent to you partial list via email. I was thinking perhaps I can blast theses positions (of gene bank accession #) but still the location which I get is not corresponding to the actual coordinates cooresponding to particular gene. Any help will be appreciated.

Pankaj kumar · 03-17-2011, 07:23 PM

Yes bret was right.
I think you need to extract specific sequence from each clone. For example
PEG3 AC006115 19 163172 163493
PEG3 AC006115 19 161667 161938
Same AC number but two different probe. You need to extract the particular region from each clone and need to do the blast search with hg19.

thanks
Pankaj

Bert · 03-18-2011, 04:14 AM

Hello Mathew,

Ok, so as far as I understand now you want to know where the region of GenBank / EMBL / DDBJ sequence AY293855 with coordinates start 140618 and stop 140769 is located on the NCBI36 (hg18) genome assembly.

I would suggest the following steps:

1 - Retrieve the sequence for AY293855
2 - Get from this sequence the sequence corresponding to bp 140618 - 140769
3 - BLAST this sequence against GRCh37 (hg19) at e.g. NCBI or Ensembl
4 - Lift the resulting coordinates over from GRCh37 (hg19) to NCBI36 (hg18)

It would of course be easier to directly BLAST to the NCBI36 (hg18) assembly, but I don't see this option in NCBI BLAST. In Ensembl it certainly isn't possible to BLAST to older assemblies.

As we have annotated several Illumina arrays in Ensembl, another option would be to do step 3 using Ensembl BLAST and then directly look in Ensembl if there are any probes mapped to your regions of interest, instead of having to use the NCBI36 (hg18) based Illumina files.

Hope this helps.

RDW · 03-18-2011, 12:37 PM

You could get the hg18 (build 36) start and end co-ordinates of accessions like AY293855 from the relevant table at NCBI:

ftp://ftp.ncbi.nih.gov/genomes/MapView/Homo_sapiens/

e.g.:

ftp://ftp.ncbi.nih.gov/genomes/MapVi...eq_extra.md.gz

(other accessions may be in other tables). If you have internal co-ordinates relative to the AY293855 sequence, you can then get the equivalent hg18 co-ordinates by simple arithmetic. However, some of the numbers quoted above are too big for the 139947 bp AY293855 sequence, so perhaps they refer to something else, like a clone or contig.

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Genomic coordinates to gene names	Layla	Bioinformatics	8	04-17-2014 03:23 PM
GenGIS, a geospatial information system for genetic and genomic data	KerryOdair	Personalized Genomics	0	10-07-2011 10:09 AM
Need Help On NCBI ref Gene coordinates File	dafil	Bioinformatics	5	02-10-2011 04:57 AM
From Affy probe sets/gene symbols to genomic coordinates?	ETHANol	Epigenetics	7	10-25-2010 03:13 AM
Gene information in Cuffdiff output files	hong_sunwoo	Bioinformatics	2	10-05-2010 06:13 AM

03-16-2011, 06:40 PM	#1
mathew Member Location: australia Join Date: Jan 2011 Posts: 81	getting genomic coordinates from gene accesion information I have list of gene accession numbers (e.g AY.... - Chr no start --- and stop ---). Is there any way that I can get genomic location of these regions in Hg18. I have tried USCS geneom browser Table that will not work. Thanks

03-17-2011, 07:59 AM	#3
mathew Member Location: australia Join Date: Jan 2011 Posts: 81	genomic coordinates What I have is Genebank accession Id (like AY293855) - Chr no (6 ) and start (140600) and stop (1407890) so I want to find out corresponding genomic coordinates in Hg18. Thanks Bert

03-17-2011, 07:43 AM	#2
Bert Junior Member Location: Cambridge, UK Join Date: Nov 2009 Posts: 8	Hello Mathew, From the title and content of your post it's not clear to me what you want to accomplish .... What data do you exactly have and what data do you want to retrieve? Cheers, Bert

03-17-2011, 08:35 AM	#4
Bert Junior Member Location: Cambridge, UK Join Date: Nov 2009 Posts: 8	Mathew, It's still not clear to me what your coordinates represent. Relative to which sequence are they? And how many of these ID's do you have? Cheers, Bert

03-17-2011, 08:40 AM	#5
Pankaj kumar Junior Member Location: Charlottesville, Virginia, USA Join Date: Aug 2010 Posts: 4	Hi, check the ucsc genome browser. http://genome.ucsc.edu/cgi-bin/hgLiftOver You need to give input as chr# start_position end_position select your assembly and you are done. Pankaj

03-17-2011, 08:48 AM	#6
Bert Junior Member Location: Cambridge, UK Join Date: Nov 2009 Posts: 8	What Matthew has are not genomic coordinates as far as I can see .... AY293855 is a sequence from the IGF2R gene, and that is located in GRCh37 (hg19) at position 160390131-160534539 (http://www.ensembl.org/Homo_sapiens/...0131-160534539). Cheers, Bert

03-17-2011, 08:51 AM	#7
Pankaj kumar Junior Member Location: Charlottesville, Virginia, USA Join Date: Aug 2010 Posts: 4	Hi Bert, He has genomic co-ordinate. see "Chr no (6 ) and start (140600) and stop (1407890)"

03-17-2011, 09:01 AM	#8
Bert Junior Member Location: Cambridge, UK Join Date: Nov 2009 Posts: 8	Pankaj, Please read my reply carefully. Mathew has a GenBank / EMBL / DDBJ ID and some coordinates. If you would look up the ID (AY293855), you would see that this is the sequence for the human IGF2R gene (http://www.ebi.ac.uk/ena/data/view/AY293855). When you then would look up where this gene is located in GRCh37 (hg19) you would see that it is on chromosome 6 at position 160390131-160534539 (http://www.ensembl.org/Homo_sapiens/...0131-160534539). Now, that are quite different numbers from 140600-1407890, right? So, the coordinates Mathew has cannot be genomic coordinates. I suspect they are relative to e.g. a clone or so. Cheers, Bert

03-17-2011, 02:26 PM	#9
mathew Member Location: australia Join Date: Jan 2011 Posts: 81	Bert, You are right I have locations which have been published in paper with the corresponding gene bank accession # (Ay...,AC.. etc) I only have handful of these. I have sent to you partial list via email. I was thinking perhaps I can blast theses positions (of gene bank accession #) but still the location which I get is not corresponding to the actual coordinates cooresponding to particular gene. Any help will be appreciated.

03-17-2011, 07:23 PM	#10
Pankaj kumar Junior Member Location: Charlottesville, Virginia, USA Join Date: Aug 2010 Posts: 4	Yes bret was right. I think you need to extract specific sequence from each clone. For example PEG3 AC006115 19 163172 163493 PEG3 AC006115 19 161667 161938 Same AC number but two different probe. You need to extract the particular region from each clone and need to do the blast search with hg19. thanks Pankaj

03-18-2011, 04:14 AM	#11
Bert Junior Member Location: Cambridge, UK Join Date: Nov 2009 Posts: 8	Hello Mathew, Ok, so as far as I understand now you want to know where the region of GenBank / EMBL / DDBJ sequence AY293855 with coordinates start 140618 and stop 140769 is located on the NCBI36 (hg18) genome assembly. I would suggest the following steps: 1 - Retrieve the sequence for AY293855 2 - Get from this sequence the sequence corresponding to bp 140618 - 140769 3 - BLAST this sequence against GRCh37 (hg19) at e.g. NCBI or Ensembl 4 - Lift the resulting coordinates over from GRCh37 (hg19) to NCBI36 (hg18) It would of course be easier to directly BLAST to the NCBI36 (hg18) assembly, but I don't see this option in NCBI BLAST. In Ensembl it certainly isn't possible to BLAST to older assemblies. As we have annotated several Illumina arrays in Ensembl, another option would be to do step 3 using Ensembl BLAST and then directly look in Ensembl if there are any probes mapped to your regions of interest, instead of having to use the NCBI36 (hg18) based Illumina files. Hope this helps.

03-18-2011, 12:37 PM	#12
RDW Member Location: London Join Date: Oct 2008 Posts: 63	You could get the hg18 (build 36) start and end co-ordinates of accessions like AY293855 from the relevant table at NCBI: ftp://ftp.ncbi.nih.gov/genomes/MapView/Homo_sapiens/ e.g.: ftp://ftp.ncbi.nih.gov/genomes/MapVi...eq_extra.md.gz (other accessions may be in other tables). If you have internal co-ordinates relative to the AY293855 sequence, you can then get the equivalent hg18 co-ordinates by simple arithmetic. However, some of the numbers quoted above are too big for the 139947 bp AY293855 sequence, so perhaps they refer to something else, like a clone or contig.