Download gene data

Question

[Peerzada]

Hello all ,

I want to download data from "http://solomics.agis.org.cn/potato/ftp/genome/" . This contains whole genome data of many potatoes. As this is huge data , I just want to download my gene of interest sequence whose chromosome no , start and end position I know .How can I download that . I want to download that gene for all the potatoes there.

Thank you

Answer 1

[Michael]

As the server stores gzip compressed data, I would say it is not possible from that resource. With uncompressed data, it may be theoretically possible to use some byte-offset shenanigans where one calculates the byte offset for a specific gene (that should be possible once one knows the length of the lines and all header lines) and then instructs the server to start downloading data from that byte-offset (this is often used for resuming failed downloads and not all servers support it). But as the files are compressed, I don't see how this could be achieved (easily). Even if they weren't, it would be extremely error-prone (a single byte more in a fasta header and everything breaks) and is not worth the effort IMO.

I recommend either downloading all the data or looking for the gene sequences by their accessions in GenBank or a specific genome browser. If they are there, you can easily get only the sequence ore your gene of interest.