About Site Map Submit Contact Us Log in | Create an account
Create an account Log In
Average Rating
User Rating:
Visitors Rating:
My rating:

Write review
See full specifications

linux default iconnebseq Publisher's description

Basic Biological Sequence Manipulations

nebseq is a Python module for basic biological sequence manipulations.

Import as usual

>>> import nebseq

Reverse complements

The only note here is that revcomp does not check the input sequence to see if it looks like DNA or RNA.

>>> nebseq.revcomp('ACGT')
>>> nebseq.revcomp('TTACC')

And if we give it garbage it just gives us garbage back.

>>> nebseq.revcomp('ZQ')


The translation function should allow for full support of sequence translation. This includes things like trimming the first couple bases and using alternate translation tables. There is also support for the more esoteric post translational modifications that can be found in some Genbank files as well as translating partial peptides (for things like fuzzy coordinates).

Basic translation:

>>> nebseq.translate('TTGGCCAAGGAACGA', table=11)

Showing the effects of a partial peptide translation. By default the first codon should be a start codon according to the selected translation table, if not then its converted to an 'X'

>>> nebseq.translate('GCCAAG')
>>> nebseq.translate('GCCAAG', partial=True)

Or we can remove the first couple of bases for fuzzy coordinates.

>>> nebseq.translate('TTGCCAAG', start=2, partial=True)

Modifications are specified as an (index, amino_acid) two-tuple. Notice that modification indexes are specified as one-based indexes into the amino acid sequence.

>>> nebseq.translate('ATGAAGGAA', modifications=[(2, 'U')])


Sequence extraction is for when you want to slice out part of a larger sequence. This is useful if you use the nebgb module and its definition of locations parsed from strings like join(1..5,9..100).

>>> location = {'type': 'span', 'from': 4, 'to': 10}
>>> nebseq.extract('ACCGTACCATAGTT', location)
('GTACCAT', (False, False))
>>> location = {
... "type": "complement",
... "segment": {
... "type": "join",
... "segments": [
... {"type": "span", "from": 3, "to": 8},
... {"type": "span", "from": 10, "to": 14}
... ]
... }
... }
>>> nebseq.extract('ACCGTATTTCGGGGACAT', location)
('CCCCGAATACG', (False, False))

System Requirements:

В· Python
Program Release Status:
Program Install Support: Install and Uninstall

Is nebseq your software?

Manage your software
There are no related downloads.

Most Popular

linux default icon Alkitab Bible Study 2.8.1
Alkitab Bible Study is a cross platform and open source bible study toolset.
linux default icon StarDict for Fedora Linux 3.0.2
A free open source off-line dictionary program that allows you to use all those free dictionaries
linux default icon Xibo 1.3.1
Xibo (pronounced eX-E-bO) is an an open source.,....
linux default icon django-webtest 1.4.4
Instant integration of Ian Bicking's WebTest with Django's testing framework
linux default icon Maitreya's Dream 6.0.3
Maitreya is a free software (GPL) for Vedic and western astrology.

Related Category

» Astrology (3)
» Astronomy (25)
» Food & Drink (2)
» Genealogy (1)
» Other (15)
» Recreation (2)
» Religion (2)