Welcome to the Genome Toolbox! I am glad you navigated to the blog and hope you find the contents useful and insightful for your genomic needs. If you find any of the entries particularly helpful, be sure to click the +1 button on the bottom of the post and share with your colleagues. Your input is encouraged, so if you have comments or are aware of more efficient tools not included in a post, I would love to hear from you. Enjoy your time browsing through the Toolbox.

Friday, May 24, 2013

Download Nucleotide Sequence for Genomic Region

Sometimes I need the nucleotide sequence for a specific region of the genome to investigate sequence similarity, simple repeats present, or recurring motifs.  I know entire chromosomal .fasta files can be downloaded from the UCSC ftp site, but then I would have to go through the entire file and hopefully extract out the correct sequence I needed.  Today I came across a very easy way to download a nucleotide sequence for a genomic region using the UCSC DAS server.  Simply modify the below web link to include the appropriate genome build and genomic coordinates and you will get a customized XML page generated with the nucleotide sequence for your query.  One word of caution: the DAS server uses an index of +1 for the first base.  Pretty cool and very simple to do.


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