JDSA is a Java program that will degenerately search DNA sequences. This program searches sequences for multiple nucleotides at a given position (positional degeneracy), limited overall sequence accuracy (group degeneracy) or variable spacing between multiple DNA sequences (spacing degeneracy). This program was designed to search the S. pombe genome or the D. melanogaster genome, but custom searches can be performed provided the input is in the correct format. This program has been written in Java 2, SDK 1.4.2_03, contains a graphical interface (Swing v 1.1) and has been tested on both a Win98/XP PC, Mac OS 9.1. and Mac OS X (10.1.4)

Necessary downloads:
For any java application, you need to have the proper virtual machine installed before an application will run. These are platform (operating system) specific, and can be obtained by following the links below.

Win 9x/2000/XP:
1. You will need to download and install the Java Runtime Environment (JRE). It is available here.
2. Download the program file (JDSAv01.jar) and run it (see instructions section below.)
3. You may also need the Java Foundation Classes (JFC)/Swing Package. That is available here.

Mac OS 9.x:
1. You will need to download and install the Macintosh Runtime for Java (MRJ) 2.2.5. It is available here.
2. You will need to download a file called swingall.jar. This file will need to be placed in the folder: System Files: Extensions: MRJ Libraries: MRJClasses
3. Download the program file and run it (see instructions section below.)

Mac OS X:
1. Download the file: JDSAv01.jar. Double-click the icon and go.

Additional Files: If you want to search an entire genome and the files are not stored locally, you must create a file containing all of the GI numbers for every genome sequence file and point the filechooser to that file. Here are the Drosophila melanogaster Release v3.2 and S. pombe genome GI lists. These may not be the most up to date annonations of the sequencing results.

1. Positional degeneracy: If you wanted to search for a DNA element that contained degeneracy at a given position - the initiator (Inr) region of Drosophila, for example. The Initiator of Drosophila is the consensus sequence from which transcription starts (the +1 of an RNA transcript.) This sequence is T-C-A-(G or T)-T-(T or C). Searching each permutation (by BLAST search for example) is very inefficient. Instead, using the standard IUPAC designation for degenerate nucleotides, the JDSA algorithm will return all permutations of the Inr sequence. For example, the above Inr sequence can be written: TCAKTY. The Downstream Promoter Element (Burke & Kadonaga(1996); Kutach & Kadonaga(2000)) would be written as: RGWYG. For more information regarding the DPE and promoters, click here.

The IUPAC degeneracy codes are below:

IUPAC	Nucleotide(s)	Complement Nucleotide(s)
A	A	T
C	C	G
G	G	C
T	T	A
M	A OR C	K
R	A OR G	Y
W	A OR T	W
S	C OR G	S
Y	C OR T	R
K	G OR T	M
V	A OR C OR G	B
H	A OR C OR T	D
D	A OR G OR T	H
B	C OR G OR T	V
N	A OR C OR T OR G	N

2. Group degeneracy: When searching for a DNA binding element, a perfect match may not be necessary because the entirety of the element may not be necessary for binding the corresponding protein. That is to say, if an element is 6 nucleotides long, sometimes a given protein that normally binds to this region will bind if there is only a 5/6 match to the consensus sequence. Binding to a perfect match versus an imperfect match could be an integral part of regulating activity. Again using the Inr region, it is possible that transcriptional machinery will bind to an Inr region if only 5/6 nucleotides are a match. In this case, we would say that the maximum allowable mismatch is 1. If you ask the JDSA program to search for a given sequence with a maximum mismatch of 1, the mismatch has the potential to appear anywhere within the sequence.

3. Spacing degeneracy: This type of degeneracy has to do with the spacing between two DNA elements. Returning to the promoter example, if you wanted to look for a TATA box that was close to an initiator, you could do so with the JDSA program. A TATA box is the most biologically pertinent when it appears further away than 30 nucleotides upstream of the initiator, and no closer than 10. To have the JDSA program search for these results, you would enter the following:
- New Search, 2 DNA elements.
- For element #1: TATAAA (the TATA box consensus) with any desired maximum allowable mismatch (see group degeneracy)
- For element #2: TCAKTY (the Drosophila Initiator sequence) with the given maximum allowable mismatch.
- For element #2: Maximum distance away from element 1 would be 30
- For element #2: Minimum distance would be 10.

Please note: the number signifies the nucleotides in between the given elements. For example, if you wanted to search element A and element B, and the end of A could be 0 nucleotides away from the start of element B, then the minimum distance would be 0.
Likewise, if the distance between two DNA elements is fixed, simply enter the same number for both the maximum and minimum distance.