I am looking for a bioinformatic website or tool to get the locations of a list of genes but in one shot instead of doing it gene by gene. Is there a way to do this? Also, if you have R script to do so, please share.
Thanks
www.biomart.org
you can "browse data":
"dataset" -> select dataset / organis [NEXT]
"filters" -> give the genes you are looking for (you can also upload a file) [NEXT]
"output" -> select the chromosome name and gene/transcript start and end position [RESULTS>]
Et voilà.
Depends on the genome you are working with. What's the target organism?
In wheat see end of list
McIntosh R.A., Yamazaki Y., Dubkovsky J., Rogers J., Morris C., Somers
D.J., Appels R., Devos K.M. Catalogue of gene symbols for wheat // 11th
Inter. Wheat Genet. Symp., Australia 2008. http://www.shigen.nig.ac.jp/wheat/
komugi/genes/symbolClassList.jsp
www.biomart.org
you can "browse data":
"dataset" -> select dataset / organis [NEXT]
"filters" -> give the genes you are looking for (you can also upload a file) [NEXT]
"output" -> select the chromosome name and gene/transcript start and end position [RESULTS>]
Et voilà.
If you interested in Human/Mouse genome then refer http://www.gencodegenes.org/stats/current.html
You can see all the genes with chromosomal location.
Check this tool too: https://genome.ucsc.edu/cgi-bin/hgTables
adding to Pilar:
the solution is for homo sapiens ("Hs"). There are similyr annotation pakckages available also for mus musculus ("Mm") and rattus norvegicus ("Rn"). It is worth havin a look into the "AnnotationData" view of the BioC packages (http://www.bioconductor.org/packages/release/BiocViews.html#___Organism)-
Biomart can also be used from within R directly (library "biomaRt").
Biomart is the best for such operation, it is also avaliable on http://www.ensembl.org/biomart/martview/508782c3bbd7b3a331da76b1d4b1119c.
If you use R, be carefull about genome version and check it independently for one or two gene to be sure if this is what you want.
If you have a list, no matter how large, but only one go with biomart as people suggest here. No need to program for such a case.
If you have not one list, but many because you will be requesting this information many times and can't compile a single list at once, then try programmatic options like those based on R, python, etc
You can also get the genomic coordinates by using table browser from UCSC Genome Bioinformatics Site (http://genome.ucsc.edu/cgi-bin/hgTables)
You can also use ProteINSIDE : www.proteinside.org
Past your IDs on a custome analysis, when it's done you will get a downloadable table with all information about your IDs (like chromosomal locations).
Thanks Nicolas, I have tried your method and it is simple but unfortunately the results were not that accurate. It gives me for example 7p15 for one input gene instead of 7p14.3. I think i can live with this for now. Thanks again
Thank you for your comment :)
We get the location of the NCBI gene sheets, I think these locations are less accurate than you hoped (maybe it's more accurate on the NCBI GeneMap).
Regards
not sure if this will help but infino.me has ability to take DNA from 23 and Me and run it showing the genes listed on chromosomes. I am brand new to learning this. 7 days old in it.
Use this function my friend org.Hs.egCHR in package "org.Hs.eg.db". these codes are from package pdf
## select() interface:
## Objects in this package can be accessed using the select() interface
## from the AnnotationDbi package. See ?select for details.
## Bimap interface:
x
Hi all
I would like to know the gene distribution in different chromosomes of c elegans. How can I do it? Anybody can help me?
A very simple solution would be to parse the annotation file.
Just use this bash command: grep -f gene_names.txt < annotation.gtf | cut -f1,3,4,5 | grep gene | cut -f1,3,4 > result.txt
gene_names.txt is the file which contains the list of genes (one per line).
This command works for this annotation file: ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_30/gencode.v30.annotation.gtf.gz
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