EMBOSS

EDIT

Sequence editing

Program name Description

biosed Replace or delete sequence sections

codcopy Reads and writes a codon usage table

cutseq Removes a specified section from a sequence

degapseq Removes gap characters from sequences

descseq Alter the name or description of a sequence

entret Reads and writes (returns) flatfile entries

extractfeat Extract features from a sequence

extractseq Extract regions from a sequence

listor Write a list file of the logical OR of two sets of sequences

maskfeat Mask off features of a sequence

maskseq Mask off regions of a sequence

newseq Type in a short new sequence

noreturn Removes carriage return from ASCII files

notseq Exclude a set of sequences and write out the remaining ones

nthseq Writes one sequence from a multiple set of sequences

pasteseq Insert one sequence into another

revseq Reverse and complement a sequence

seqret Reads and writes (returns) sequences

seqretsplit Reads and writes (returns) sequences in individual files

skipseq Reads and writes (returns) sequences, skipping first few

splitter Split a sequence into (overlapping) smaller sequences

trimest Trim poly-A tails off EST sequences

trimseq Trim ambiguous bits off the ends of sequences

union Reads sequence fragments and builds one sequence

vectorstrip Strips out DNA between a pair of vector sequences

yank Reads a sequence range, appends the full USA to a list file

Program name	Description
biosed	Replace or delete sequence sections
codcopy	Reads and writes a codon usage table
cutseq	Removes a specified section from a sequence
degapseq	Removes gap characters from sequences
descseq	Alter the name or description of a sequence
entret	Reads and writes (returns) flatfile entries
extractfeat	Extract features from a sequence
extractseq	Extract regions from a sequence
listor	Write a list file of the logical OR of two sets of sequences
maskfeat	Mask off features of a sequence
maskseq	Mask off regions of a sequence
newseq	Type in a short new sequence
noreturn	Removes carriage return from ASCII files
notseq	Exclude a set of sequences and write out the remaining ones
nthseq	Writes one sequence from a multiple set of sequences
pasteseq	Insert one sequence into another
revseq	Reverse and complement a sequence
seqret	Reads and writes (returns) sequences
seqretsplit	Reads and writes (returns) sequences in individual files
skipseq	Reads and writes (returns) sequences, skipping first few
splitter	Split a sequence into (overlapping) smaller sequences
trimest	Trim poly-A tails off EST sequences
trimseq	Trim ambiguous bits off the ends of sequences
union	Reads sequence fragments and builds one sequence
vectorstrip	Strips out DNA between a pair of vector sequences
yank	Reads a sequence range, appends the full USA to a list file