Sputnik source code history...

The source code from sputnik has been adapted by several authors before.

The original source code contained the main SSR  searching algorithm
and was written by Chris Abajian from the Univ. Washington at Seattle back in 1994.
You can obtain this original version from http://rast.abajian.com/sputnik/

I found this modifyed source version from the University of Delaware 
(http://capb.dbi.udel.edu/main/tools.htm), where Hanafey, et al. deposited their version 
used for the publication in Nature Genetics, 2002.

The folks from U.Delaware (and from Dupont, INC) made significant improvements in the code
to make it run faster and to report SSR motives in a more consistent way (like reporting  
original motives, frame variants and their reverse complements as the same motif). They also 
added command line options.

However they left the output format as in the original version, which meant you had to write
a parser anyway.  This is where I came in:  I changed a couple of things to make the source code 
easier to compile under Windows, included the windows versions  of the files 'getOpt.h' and 'getOpt.c'
that read the command line options, changed the parsing of the FASTA sequence headers to deal with
GenBank style Fasta headers  and modifyed the output so that it writes the report in a
TAB-delimited format, which is easier to import directly into a relational database.

Included is a Microsoft Visual C++ 6.0 project that can be used to compile the code. 

This is the source version of march-2003.

Mauricio La Rota
Plant Breeding Dept.
Cornell University.

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Example of output from the three versions of Sputnik.  The fourth is an example showing my
favorite command line flags.

1) --------------------------------
  original_sputnik.exe test.fasta

>test1
dinucleotide 15 : 27 -- length 13 score 11
GCGCGCGCGCGCG
dinucleotide 34 : 45 -- length 12 score 10
GCGCGCGCGCGC
>test2
dinucleotide 79 : 92 -- length 14 score 12
CGCGCGCGCGCGCG

2) --------------------------------
  sputnik_DuPont_orig.exe test.fasta

>test1
dinucleotide 15 : 26 -- length 12 score 10 unit CG
GCGCGCGCGCGC
dinucleotide 34 : 45 -- length 12 score 10 unit CG
GCGCGCGCGCGC
>test2
dinucleotide 79 : 92 -- length 14 score 12 unit CG
CGCGCGCGCGCGCG

3) --------------------------------
  sputnik.exe test.fasta

#
# SEQID--REP_TYPE--SSRSTART--SSREND--SSRLEN--SCORE--MOTIF--SSR_SEQ
#

test1   dinucleotide    15      26      12      10      CG      GCGCGCGCGCGC
test1   dinucleotide    34      45      12      10      CG      GCGCGCGCGCGC
test2   dinucleotide    79      92      14      12      CG      CGCGCGCGCGCGCG

4) --------------------------------
  sputnik.exe -v 2 -A -n -6 -s 8 -p -j -L 10 -l -1 test.fasta

#
# SEQID--REP_TYPE--SSRSTART--SSREND--SSRLEN--SCORE--MOTIF--SSR_SEQ
#

test1   dinucleotide    15      26      12      100     CG      GCGCGCGCGCGC
test2   tetranucleotide 42      49      8       100     AGCT    TAGCTAGC
test2   dinucleotide    79      92      14      100     CG      CGCGCGCGCGCGCG