Parameter

Description

contigs:{1 2 3}

Applies the command to contigs 1, 2, and 3.

contigs:{1 (460>960) 2 (200>2000)}

Applies the command to only a segment of each contig.

sequencesInContigs:{"filename1.ext" "filename2.ext" "filename3.ext"}

Applies the command to the contig(s) in which the named sequences are located.

The following optional values let you specify that only a subset of the contig be considered. They are placed after the contig number or filename:

contigs:all

Applies the command to all contigs.

contigs:none

Does not apply the command to any of the contigs.

contigs:where {group=n}

Applies the command to contigs whose scaffold relates to a specified scaffold “n”.* This parameter could be used when you have manually scaffolded contigs together (e.g. based on dual-end data) or after assembly, when deleting or exporting sequences.

contigs:where {length=n}

Applies the command to contigs whose length relates to a specified number “n”.*

contigs:where {number>n}

Applies the command to contigs whose total number of sequences relates to a specified number “n”.*

contigs:where {position<n}

Applies the command to contigs whose position relates to a specified position “n”.* This parameter could be used when you have manually ordered contigs in a particular scaffold (e.g., based on dual-end data), or after assembly, when deleting or exporting sequences.

endpnt:(49>538)

Applies the command to the segment of the contig between the specified coordinates. The paired parentheses must be enclosed in quotes.

endpnt:(lend>rend)

Applies the command from the left end to the right end of the contig (i.e., the entire contig). This works the same as omitting the endpnt parameter entirely. The paired parentheses must be enclosed in quotes.