I am trying to download detailed information about a genomic region, but not getting any way to download it. My requirement includes: intronic, exonic and both 3'-utr and 5'utr coordinates for all available transcripts. Also the DNA, cDNA and protein sequence including strand information. Any other information of the gene will be an added advantage. More importantly I need it for a region in a single step. Is there any way of doing it?
You can also try with Ensembl!
http://www.ensembl.org/index.html
It´s pretty easy to dowlnoad genetic information of several genomes (human, mouse zebrafish...)
Potentially you could also use the KEGG database as it lets you specify locations in the genome, but it depends on the type of information you want http://www.genome.jp/kegg/
@ Rohan,
I have tried UCSC. Coordinates I am getting from there, but not the sequences. If you are aware can you please elaborate.
@ Francisco:
I have tried Ensembl too but not finding it exactly. May be some scripts can serve the purpose.
genebank or ncbi/gene is the best option. u can download all th info u need. additionally u can browse gene card web site.
1. Go to http://www.ensembl.org/index.html
2. Select your genome (GRCh37 for human)
3. Select your gene or the coordinates of your transcript
4. Click Export Data
5. Select all the genetic information that you need: flanking sequences, cDNA, coding sequence, UTRs, exons, introns...
Hope it works!
There is probably no need to write scripts when using the UCSC Table Browser. It has optional "sequence" output format, in addition to BED or GTF, which outputs a multifasta file with coordinates in the headers.
- Badges
- Science topic
- Similar topics
- Computer Science and Engineering
- Bioinformatics
- Bioinformatic Tools