This web tool allows extraction of DNA sequence from the SGRP assemblies. 
by Alan Moses and Alex Nguyen Ba (2008)


Instructions
1) Select the species of interest by clicking either ‘S. cer.’ for S. cerevisiae or ‘S. par.’ for S. paradoxus. 
2) Enter the coordinates for the genomic regions of interest in the box (see format description below)
3) Click the ‘extract’ button below.  The browser will automatically direct you to a page displaying the DNA sequence 

Input format for coordinates

The web tool allows two formats for coordinates to be pasted into the box, and we describe each below

(i) 4 column format.  This format contains the name of the strain, the chromosome and the start and stop in 4 columns.  These must be separated by spaces or tabs. For example, 

REF chr12 290213 291937

Retrieves coordinates 290213-291937 on chromosome 12 of the reference genomes strain.

(ii) Blast output format.  For convenience, we also allow direct input from the BLAST server on the left side of the page. Pasting

gal2	S288c.chr12	100.00	1725	0	0	1	1725	291673	293397	0.0	3378

Into the box retrieves coordinates 291673-293397 on chromosome 12 for S288c.  For further convenience, if the ‘Linked Table’ BLAST display has been selected, lines from the BLAST output can be added to the sequence extraction tool simply by clicking the lines.

Finally, we note that the sequence extraction tool allows up to 50 sequences to be extracted simultaneously.  Each set of coordinates should be listed as a new line in the text box.  For example, entering

REF	chr12	290213	291937
S288c	chr12	291673	293397
378604X	chr12	289757	291481		

Or 

gal2	S288c.chr12	100.00	1725	0	0	1	1725	291673	293397	0.0	3378
gal2	REF.chr12	100.00	1725	0	0	1	1725	290213	291937	0.0	3378
gal2	378604X.chr12	99.77	1725	4	0	1	1725	289757	291481	0.0	3346

Will retrieve a multiple fasta file containing all of these sequences.

>378604X.chr12 289757 - 291481
ATGGCAGTTGAGGAGAACAATATGCCTGTTGTTTCACAGCAACCCCAAG...
>REF.chr12 290213 - 291937
ATGGCAGTTGAGGAGAACAATATGCCTGTTGTTTCACAGCAACCCCAAG...
>S288c.chr12 291673 - 293397
ATGGCAGTTGAGGAGAACAATATGCCTGTTGTTTCACAGCAACCCCAAG...