Question: Gen Map In Chromosomes Of Humans
0
gravatar for Dilshan
7.7 years ago by
Dilshan0
Dilshan0 wrote:

I am trying to create a gene map as to how the genes are organised in a particular Chromosome of humans. For this I require the start and positions (locations) of the gene in the respective chromosome. The NCBI has the data file seq_contig.md.gz (ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/) containing similar information. But the readme file does not contain adequate information as to the exact content in this file.

Therefore could you please let me know if this file contains the correct information that I am looking if not what is the most appropriate resource for this information.

human • 1.7k views
ADD COMMENTlink modified 5.2 years ago by Biostar ♦♦ 20 • written 7.7 years ago by Dilshan0

There are already many questions on this site related to "finding the coordinates of some genes".

ADD REPLYlink written 7.7 years ago by Pierre Lindenbaum118k

You should also look around for existing tools. I depends a bit on your purpose . But it might very well be that existing genome browser already allow you to do what you want to do, or that you can at least use existing code as a starting point. There is nothing against reinventing the wheel if you produce a better wheel, but it is good to look at existing wheels first.

ADD REPLYlink written 7.7 years ago by Chris Evelo10.0k

You should also look around for existing tools. I depends a bit on your purpose, but it might very well be that existing genome browser already allow you to do what you want to do, or that you can at least use existing code as a starting point. There is nothing against reinventing the wheel if you produce a better wheel, but it is good to look at existing wheels first.

ADD REPLYlink written 7.7 years ago by Chris Evelo10.0k
3
gravatar for Neilfws
7.7 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

I'd start from the NCBI Map Viewer page for human. Choose your chromosome, scroll down to the summary info and see if any of the Download/View Sequence/Evidence links contain what you want.

It's probably a good idea to read some of the Map Viewer documentation too.

ADD COMMENTlink written 7.7 years ago by Neilfws48k

Thanks a lot neilfws, you were spot on.

ADD REPLYlink written 7.7 years ago by Dilshan0
1
gravatar for Maxime Lamontagne
7.7 years ago by
Québec
Maxime Lamontagne2.1k wrote:

Try UCSC genome browser:

http://genome.ucsc.edu/ Tables -group: Genes and Gene Prediction Tracks -track: UCSC Genes -position: chr? (chr1, chr2, ...) -output file: ??? (output.txt)

get output Select Fields from hg18.knownGene: -name -cdsStart -cdsEnd hg18.kgXref fields: -geneSymbol

ADD COMMENTlink written 7.7 years ago by Maxime Lamontagne2.1k

Thanks a lot Baboune.

ADD REPLYlink written 7.7 years ago by Dilshan0
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