eliminACE: mask redundant fragments in a set of nucleic acid sequences

This program BLASTs a set of nucleic acid sequences against each other, reports fragments shared by sequences in the set, and masks all but one instance. It does not mask repeats within the same sequence. When two sequences have a common fragment, the fragment is masked in the sequence with the name that is alphabetically greater.

Inputs:

1. a file of sequences in FASTA format; the program halts if a sequence doesn't have a name or two sequences share a name;
2. a BLAST e-value; the lower the value, the more significant the matches must be to be reported.

Output:

A file of sequences in FASTA format, with the redundant fragments masked, i.e., replaced by N's.

Enter sequence file name 

BLAST E-value          lower = more stringent

gapped BLAST    

mask low-complexity regions before BLASTing then restore them    

When the results appear, use File/Save As.

1/16/2000 adnan@genetics.med.harvard.edu