fasta-center [options]


Reads sequences in FASTA format. For each sequence, it outputs the central portion of the sequence. The flanking regions can also be output to a separate file. When the alphabet is specified and the central portion of a sequence consists of nothing but the wildcard it is not output.


Sequences in FASTA format from standard input.


Writes a FASTA format file to standard output.


Option Parameter Description Default Behavior
Alphabet Options
General Options
-lenlen Length of central region to output. If this is larger than the length of a sequence, the entire sequence is output. 100
-flankfilename Output the regions flanking the central regions to a file named filename. The FASTA IDs of the flanking regions on the left (right) are the original FASTA ID with '-L' ('-R') appended. Flanking regions are not output.
-rejectfilename Output any rejected central regions to a file named filename. Rejected central regions are not output.