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.
http://genome.ucsc.edu/cgi-bin/das/hg19/dna?segment=chr1:100000,200000
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