diffseq takes two overlapping, nearly identical sequences and reports the differences between them, together with any features that overlap with these regions.

Here is a sample session with diffseq:

% diffseq tembl:ap000504 tembl:af129756
Find differences (SNPs) between nearly identical sequences
Word size [10]:
Output file [ap000504.diffseq]:

Mandatory qualifiers:

[-asequence] (sequence)

Sequence USA.

[-bsequence] (sequence)

Sequence USA.

-wordsize (integer)

Word size.

-outfile (report)

Output report file.

Optional qualifiers:

-afeatout (featout)

File for output of first sequence's normal tab delimited gff's.

-bfeatout (featout)

File for output of second sequence's normal tab delimited gff's.

-columns (boolean)

The default format for the output report file is to have several lines per difference giving the sequence positions, sequences, and features. If this option is set to true, the output report file format is changed to a set of columns and no feature information is given.