A set of small wrapper scripts around the EMBOSS biology toolset.
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README.rst
gibson
readme
seq-abstract
seq-align-many
seq-ascii
seq-circular
seq-complement
seq-convert
seq-design-primer
seq-ends
seq-extract
seq-features
seq-find
seq-find-primer-pair
seq-len
seq-name
seq-ncbi-blast
seq-pcr
seq-pcr-tails
seq-raw
seq-rc
seq-restriction-sites
seq-reverse
seq-seq
seq-split
seq-tms
seq-to-genbank

README.rst

seq

A set of small wrapper scripts around the EMBOSS biology toolset.

For examples see https://github.com/jireva/knockout-adaptability .

Conventions

.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.

Programs

Conversions
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.
Information
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
Manipulations
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
Derrivations
seq-design-primer:Design a pcr primer
seq-ends:view just the ends of the sequence