This archive contains the results of three nucleotide sequence queries
using SSEARCH, FASTA, and BLAST.  Each of the queries were made against
nucleotide data sets available from GenBank.  The data sets used were,
the E. coli data set, the yeast data set, and the homosapien chromosome
one.  The data sets were each obtained with the November 1999 updates.

For an analysis of the results, please refer to
http://www.cs.ucsb.edu/~mdipper/dna/DNApaper.html

The following is a brief description of the files contained in this
archive:

File Name        Description
------------     -----------
BLAST.BAT        MS-DOS Batch file to run the BLAST searches
BLAST1.BAT       MS-DOS Batch file to run the query 1 BLAST searches
BLAST2.BAT       MS-DOS Batch file to run the query 2 BLAST searches
BLAST3.BAT       MS-DOS Batch file to run the query 3 BLAST searches
FASTA.BAT        MS-DOS Batch file to run the FASTA searches
SSEARCH.BAT      MS-DOS Batch file to run the SSEARCH searches

CR.TXT           File of carriage returns for FASTA and SSEARCH input
NULL.TXT         Empty file for BLAST input

QUERY1.TXT       25 nucleotide query containing a subsequence found in
                 the homosapien chromosome one data set
QUERY2.TXT       50 nucleotide query containing a subsequence found in
                 the yeast data set
QUERY2.TXT       100 nucleotide query containing a subsequence found in
                 the E. coli data set

BEQ1.TXT         BLAST search on E. Coli data set for query 1
BEQ2.TXT         BLAST search on E. Coli data set for query 2
BEQ3.TXT         BLAST search on E. Coli data set for query 3
BYQ1.TXT         BLAST search on yeast data set for query 1
BYQ2.TXT         BLAST search on yeast data set for query 2
BYQ3.TXT         BLAST search on yeast data set for query 3
BHQ1.TXT         BLAST search on homosapien data set for query 1
BHQ2.TXT         BLAST search on homosapien data set for query 2
BHQ3.TXT         BLAST search on homosapien data set for query 3

FEQ1.TXT         FASTA search on E. Coli data set for query 1
FEQ2.TXT         FASTA search on E. Coli data set for query 2
FEQ3.TXT         FASTA search on E. Coli data set for query 3
FEQ1.TXT         FASTA search on yeast data set for query 1
FYQ2.TXT         FASTA search on yeast data set for query 2
FYQ3.TXT         FASTA search on yeast data set for query 3
FHQ1.TXT         FASTA search on homosapien data set for query 1
FHQ2.TXT         FASTA search on homosapien data set for query 2
FHQ3.TXT         FASTA search on homosapien data set for query 3

SEQ1.TXT         SSEARCH search on E. Coli data set for query 1
SEQ2.TXT         SSEARCH search on E. Coli data set for query 2
SEQ3.TXT         SSEARCH search on E. Coli data set for query 3
SYQ1.TXT         SSEARCH search on yeast data set for query 1
SYQ2.TXT         SSEARCH search on yeast data set for query 2
SYQ3.TXT         SSEARCH search on yeast data set for query 3
SHQ1.TXT         SSEARCH search on homosapien data set for query 1
SHQ2.TXT         SSEARCH search on homosapien data set for query 2
SHQ3.TXT         SSEARCH search on homosapien data set for query 3
