Software Tools :: Sequence Creation and Manipulation
Background
Sequence Creation and Manipulation
Programs
- GCG Programs
- Assemble: Concatenates sequence fragments into a single sequence
- Reverse: Reverses and/or complements a sequence
- Seg: Replaces low complexity regions in protein sequences with X characters
- Xnu: Replaces statistically significant tandem repeats in protein sequences with X characters
- Simplify: Converts all symbols of the same type to the same symbol (e.g., to treat all hydrophobic amino acids as equivalent)
- Shuffle: Randomizes the order of the symbols in a sequence without changing its composition
- HmmerEmit: Generates new sequences that match a profile hidden Markov model
- Corrupt: Randomly introduces small numbers of substitutions, insertions, and deletions into a sequence
- Sample: Randomly extracts sequence fragments from sequence(s) to created new sequences
- EMBOSS Programs
- newseq: Creates a short new sequence from keyboard entry
- revseq: Reverses and complements a sequence
- trimseq: Trims ambiguous bits off the ends of sequences
- cutseq: Removes a specified section from a sequence
- extractseq: Extracts regions from a sequence
- pasteseq: Inserts one sequence into another
- splitter: Splits a sequence into (overlapping) smaller sequences
- maskseq: Masks off regions of a sequence
- maskfeat: Masks off features of a sequence
- coderet: Extracts CDS, mRNA and translations from feature tables
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