Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases

wordmatch finds all exact matches of a given minimum size between 2 sequences displaying the start points in each sequence and the match length.

Here is a sample session with wordmatch:

% wordmatch tsw:hba_human tsw:hbb_human Finds all exact matches of a given size between 2 sequences Word size [4]: Output alignment [hba_human.wordmatch]:

Mandatory qualifiers:

[-asequence] (sequence)

Sequence USA.

[-bsequence] (sequence)

Sequence USA.

-wordsize (integer)

Word size.

[-outfile] (align)

Output alignment filename.

Advanced qualifiers:

-afeatout (featout)

File for output of normal tab-delimited GFF features.

-bfeatout (featout)

File for output of normal tab-delimited GFF features.