8.9 years ago by
Suppose you want to fetch sequences of homologous promoters for all
Drosophila genes. Here is an outline of how to do this:
1. Download coordinates of flybase genes from Drosophila melanogaster
dm2 genome build (see attached images 1 and 2).
2. Use "Operate on Genomic Intervals -> Get Flanks" to convert
coordinates of genes into coordinates of putative promoters by taking
500 bp upstream of each gene (see attached images 3).
3. Use "Fetch alignments -> Stitch MAF blocks" to retrieve homologous
sequences for several species (see attached image 4).
You will get alignments in FASTA format corresponding to your
promoters. They will look like this:
Let us know you have problems.