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