A set of small wrapper scripts around the EMBOSS biology toolset.
For examples see https://github.com/jireva/knockout-adaptability .
.seq files consist of a csv feature table followed by a fasta sequence.
csv feature tables contain 1 line per feature in the following format:
name1 start stop name2 start stop
For sequences on the forward strand, start < stop. The opposite is true for sequences on the reverse strand. The other fields can contain anything you care to include. That's it.
All programs accept input on stdin and write to stdout. Some, such as seq-rc, will also treat their arguments as DNA sequences.
seq-format: convert from emboss formats to seq seq-unformat: convert from seq to genbank seq-seq: split the fasta from a seq file seq-features: split the features from the seq file seq-split: split a seq into a features table and a fasta sequence, return both file names seq-raw: return the raw nucleotides, no formatting, no whitespace.
seq-len: return the length of the sequence seq-find: find argument sequences in seq and add them to the features seq-find-primer-pair: find argument primer sequences in seq and add them to the features seq-abstract: print an abstract representation of a sequences features seq-ncbi-blast: open a browser onto a blast search for the input sequence seq-tms: measure the melting temperatures of sequences
seq-circular: append the sequence to itself to simulate a circular sequence seq-extract: extract the named feature from the sequence seq-pcr: simulate a pcr reaction seq-pcr-tails: simulate a pcr reaction with tailed primers seq-name: Add a name to the sequence seq-rc: reverse complement a sequence seq-restriction-sites: map restriction sites on a sequence
seq-design-primer: Design a pcr primer seq-ends: view just the ends of the sequence